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  1. Article ; Online: Lucas Pelkmans: taking it from the top. Interview by Ben Short.

    Pelkmans, Lucas

    The Journal of cell biology

    2009  Volume 185, Issue 6, Page(s) 932–933

    MeSH term(s) Computer Simulation ; Education, Graduate ; Endocytosis/physiology ; Humans ; Research Personnel ; Systems Biology ; Virus Internalization
    Language English
    Publishing date 2009-06-15
    Publishing country United States
    Document type Interview
    ZDB-ID 218154-x
    ISSN 1540-8140 ; 0021-9525
    ISSN (online) 1540-8140
    ISSN 0021-9525
    DOI 10.1083/jcb.1856pi
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  2. Article ; Online: Mechanisms of cellular mRNA transcript homeostasis.

    Berry, Scott / Pelkmans, Lucas

    Trends in cell biology

    2022  Volume 32, Issue 8, Page(s) 655–668

    Abstract: For most genes, mRNA transcript abundance scales with cell size to ensure a constant concentration. Scaling of mRNA synthesis rates with cell size plays an important role, with regulation of the activity and abundance of RNA polymerase II (Pol II) now ... ...

    Abstract For most genes, mRNA transcript abundance scales with cell size to ensure a constant concentration. Scaling of mRNA synthesis rates with cell size plays an important role, with regulation of the activity and abundance of RNA polymerase II (Pol II) now emerging as a key point of control. However, there is also considerable evidence for feedback mechanisms that kinetically couple the rates of mRNA synthesis, nuclear export, and degradation to allow cells to compensate for changes in one by adjusting the others. Researchers are beginning to integrate results from these different fields to reveal the mechanisms underlying transcript homeostasis. This will be crucial for moving beyond our current understanding of relative gene expression towards an appreciation of how absolute transcript levels are linked to other aspects of the cellular phenotype.
    MeSH term(s) Active Transport, Cell Nucleus ; Homeostasis/genetics ; RNA Polymerase II/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Transcription, Genetic
    Chemical Substances RNA, Messenger ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2022-05-31
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 30122-x
    ISSN 1879-3088 ; 0962-8924
    ISSN (online) 1879-3088
    ISSN 0962-8924
    DOI 10.1016/j.tcb.2022.05.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Liquid droplets in the skin.

    Rai, Arpan / Pelkmans, Lucas

    Science (New York, N.Y.)

    2020  Volume 367, Issue 6483, Page(s) 1193–1194

    Language English
    Publishing date 2020-03-12
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abb0060
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  4. Article ; Online: Iterative Indirect Immunofluorescence Imaging (4i) on Adherent Cells and Tissue Sections.

    Kramer, Bernhard A / Del Castillo, Jacobo Sarabia / Pelkmans, Lucas / Gut, Gabriele

    Bio-protocol

    2023  Volume 13, Issue 13, Page(s) e4712

    Abstract: Highly multiplexed protein measurements from multiple spatial scales using fluorescence microscopy recently emerged as a powerful way to investigate tumor microenvironments in biomedicine and the multivariate nature of complex systems' interactions. A ... ...

    Abstract Highly multiplexed protein measurements from multiple spatial scales using fluorescence microscopy recently emerged as a powerful way to investigate tumor microenvironments in biomedicine and the multivariate nature of complex systems' interactions. A range of methods for this exist, which either rely on directly labeling the primary antibody with oligonucleotides/rare metals or employing methods to remove fluorescence for cyclic acquisition. Here, we describe a protocol that uses off-the-shelf primary and secondary antibodies without further need for modification and only commonly available chemical reagents. The method harnesses the observation that antibodies can crosslink to bound epitopes during light exposure, thus preventing elution. By utilizing a simple oxygen radical scavenging buffer during imaging and by blocking free sulfhydryl groups before antibody incubation, the presented method can employ comparably mild conditions to remove bound antibodies from epitopes, which preserves sample integrity. Thus, with the stated minor modifications, it allows for a standard immunofluorescence imaging protocol in cyclic fashion, currently permitting staining of up to ~80 unique epitopes.
    Language English
    Publishing date 2023-07-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325 ; 2331-8325
    ISSN (online) 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.4712
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  5. Article ; Online: Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells.

    Berry, Scott / Müller, Micha / Rai, Arpan / Pelkmans, Lucas

    Cell systems

    2022  Volume 13, Issue 6, Page(s) 454–470.e15

    Abstract: RNA concentration homeostasis involves coordinating RNA abundance and synthesis rates with cell size. Here, we study this in human cells by combining genome-wide perturbations with quantitative single-cell measurements. Despite relative ease in ... ...

    Abstract RNA concentration homeostasis involves coordinating RNA abundance and synthesis rates with cell size. Here, we study this in human cells by combining genome-wide perturbations with quantitative single-cell measurements. Despite relative ease in perturbing RNA synthesis, we find that RNA concentrations generally remain highly constant. Perturbations that would be expected to increase nuclear mRNA levels, including those targeting nuclear mRNA degradation or export, result in downregulation of RNA synthesis. This is associated with reduced abundance of transcription-associated proteins and protein states that are normally coordinated with RNA production in single cells, including RNA polymerase II (RNA Pol II) itself. Acute perturbations, elevation of nuclear mRNA levels, and mathematical modeling indicate that mammalian cells achieve robust mRNA concentration homeostasis by the mRNA-based negative feedback on transcriptional activity in the nucleus. This ultimately acts to coordinate RNA Pol II abundance with nuclear mRNA degradation and export rates and may underpin the scaling of mRNA abundance with cell size.
    MeSH term(s) Animals ; Feedback ; Homeostasis/genetics ; Humans ; Mammals/genetics ; RNA ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Nuclear ; Transcription, Genetic/genetics
    Chemical Substances RNA, Messenger ; RNA, Nuclear ; RNA (63231-63-0) ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2022-05-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2854138-8
    ISSN 2405-4720 ; 2405-4712
    ISSN (online) 2405-4720
    ISSN 2405-4712
    DOI 10.1016/j.cels.2022.04.005
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  6. Article ; Online: Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps.

    Spitzer, Hannah / Berry, Scott / Donoghoe, Mark / Pelkmans, Lucas / Theis, Fabian J

    Nature methods

    2023  Volume 20, Issue 7, Page(s) 1058–1069

    Abstract: Highly multiplexed imaging holds enormous promise for understanding how spatial context shapes the activity of the genome and its products at multiple length scales. Here, we introduce a deep learning framework called CAMPA (Conditional Autoencoder for ... ...

    Abstract Highly multiplexed imaging holds enormous promise for understanding how spatial context shapes the activity of the genome and its products at multiple length scales. Here, we introduce a deep learning framework called CAMPA (Conditional Autoencoder for Multiplexed Pixel Analysis), which uses a conditional variational autoencoder to learn representations of molecular pixel profiles that are consistent across heterogeneous cell populations and experimental perturbations. Clustering these pixel-level representations identifies consistent subcellular landmarks, which can be quantitatively compared in terms of their size, shape, molecular composition and relative spatial organization. Using high-resolution multiplexed immunofluorescence, this reveals how subcellular organization changes upon perturbation of RNA synthesis, RNA processing or cell size, and uncovers links between the molecular composition of membraneless organelles and cell-to-cell variability in bulk RNA synthesis rates. By capturing interpretable cellular phenotypes, we anticipate that CAMPA will greatly accelerate the systematic mapping of multiscale atlases of biological organization to identify the rules by which context shapes physiology and disease.
    MeSH term(s) Cluster Analysis ; RNA
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2023-05-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-023-01894-z
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  7. Article ; Online: DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites.

    Gallo, Raffaella / Rai, Arpan Kumar / McIntyre, Alexa B R / Meyer, Katrina / Pelkmans, Lucas

    Developmental cell

    2023  Volume 58, Issue 19, Page(s) 1880–1897.e11

    Abstract: The dual-specificity kinase DYRK3 controls the formation and dissolution of multiple biomolecular condensates, regulating processes including stress recovery and mitotic progression. Here, we report that DYRK3 functionally interacts with proteins ... ...

    Abstract The dual-specificity kinase DYRK3 controls the formation and dissolution of multiple biomolecular condensates, regulating processes including stress recovery and mitotic progression. Here, we report that DYRK3 functionally interacts with proteins associated with endoplasmic reticulum (ER) exit sites (ERESs) and that inhibition of DYRK3 perturbs the organization of the ERES-Golgi interface and secretory trafficking. DYRK3-mediated regulation of ERES depends on the N-terminal intrinsically disordered region (IDR) of the peripheral membrane protein SEC16A, which co-phase separates with ERES components to form liquid-like condensates on the surface of the ER. By modulating the liquid-like properties of ERES, we show that their physical state is essential for functional cargo trafficking through the early secretory pathway. Our findings support a mechanism whereby phosphorylation by DYRK3 and its reversal by serine-threonine phosphatases regulate the material properties of ERES to create a favorable physicochemical environment for directional membrane traffic in eukaryotic cells.
    Language English
    Publishing date 2023-08-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2023.08.005
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  8. Article ; Online: Multimodal perception links cellular state to decision-making in single cells.

    Kramer, Bernhard A / Sarabia Del Castillo, Jacobo / Pelkmans, Lucas

    Science (New York, N.Y.)

    2022  Volume 377, Issue 6606, Page(s) 642–648

    Abstract: Individual cells make decisions that are adapted to their internal state and surroundings, but how cells can reliably do this remains unclear. To study the information processing capacity of human cells, we conducted multiplexed quantification of ... ...

    Abstract Individual cells make decisions that are adapted to their internal state and surroundings, but how cells can reliably do this remains unclear. To study the information processing capacity of human cells, we conducted multiplexed quantification of signaling responses and markers of the cellular state. Signaling nodes in a network displayed adaptive information processing, which led to heterogeneous growth factor responses and enabled nodes to capture partially nonredundant information about the cellular state. Collectively, as a multimodal percept this gives individual cells a large information processing capacity to accurately place growth factor concentration within the context of their cellular state and make cellular state-dependent decisions. Heterogeneity and complexity in signaling networks may have coevolved to enable specific and context-aware cellular decision-making in a multicellular setting.
    MeSH term(s) Epidermal Growth Factor/pharmacology ; Epithelial Cells/drug effects ; Epithelial Cells/physiology ; Humans ; Signal Transduction ; Single-Cell Analysis
    Chemical Substances Epidermal Growth Factor (62229-50-9)
    Language English
    Publishing date 2022-07-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abf4062
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  9. Article ; Online: Cellular state landscape and herpes simplex virus type 1 infection progression are connected.

    Pietilä, Maija K / Bachmann, Jana J / Ravantti, Janne / Pelkmans, Lucas / Fraefel, Cornel

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 4515

    Abstract: Prediction, prevention and treatment of virus infections require understanding of cell-to-cell variability that leads to heterogenous disease outcomes, but the source of this heterogeneity has yet to be clarified. To study the multimodal response of ... ...

    Abstract Prediction, prevention and treatment of virus infections require understanding of cell-to-cell variability that leads to heterogenous disease outcomes, but the source of this heterogeneity has yet to be clarified. To study the multimodal response of single human cells to herpes simplex virus type 1 (HSV-1) infection, we mapped high-dimensional viral and cellular state spaces throughout the infection using multiplexed imaging and quantitative single-cell measurements of viral and cellular mRNAs and proteins. Here we show that the high-dimensional cellular state scape can predict heterogenous infections, and cells move through the cellular state landscape according to infection progression. Spatial information reveals that infection changes the cellular state of both infected cells and of their neighbors. The multiplexed imaging of HSV-1-induced cellular modifications links infection progression to changes in signaling responses, transcriptional activity, and processing bodies. Our data show that multiplexed quantification of responses at the single-cell level, across thousands of cells helps predict infections and identify new targets for antivirals.
    MeSH term(s) Humans ; Herpesvirus 1, Human/physiology ; Herpes Simplex ; Antiviral Agents/metabolism ; RNA, Messenger/metabolism ; Virus Replication
    Chemical Substances Antiviral Agents ; RNA, Messenger
    Language English
    Publishing date 2023-07-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-40148-6
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  10. Article ; Online: Cell Biology. Using cell-to-cell variability--a new era in molecular biology.

    Pelkmans, Lucas

    Science (New York, N.Y.)

    2012  Volume 336, Issue 6080, Page(s) 425–426

    MeSH term(s) Animals ; Cell Biology ; Cell Communication ; Cell Physiological Phenomena ; Cells, Cultured ; Cellular Microenvironment ; Cytological Techniques ; Humans ; Molecular Biology/methods ; Phenotype ; Single-Cell Analysis
    Language English
    Publishing date 2012-04-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.1222161
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