1
|
Stelloo S, Alejo-Vinogradova MT, van Gelder CAGH, Zijlmans DW, van Oostrom MJ, Valverde JM, Lamers LA, Rus T, Sobrevals Alcaraz P, Schäfers T, Furlan C, Jansen PWTC, Baltissen MPA, Sonnen KF, Burgering B, Altelaar MAFM, Vos HR, Vermeulen M. Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics. Cell Stem Cell 2024:S1934-5909(24)00144-9. [PMID: 38754429 DOI: 10.1016/j.stem.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 01/10/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Gastrulation is a critical stage in embryonic development during which the germ layers are established. Advances in sequencing technologies led to the identification of gene regulatory programs that control the emergence of the germ layers and their derivatives. However, proteome-based studies of early mammalian development are scarce. To overcome this, we utilized gastruloids and a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho) protein expression during gastruloid differentiation. Our findings revealed many proteins with temporal expression and unique expression profiles for each germ layer, which we also validated using single-cell proteomics technology. Additionally, we profiled enhancer interaction landscapes using P300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron-based perturbations combined with single-cell RNA sequencing (scRNA-seq) identified a critical role for ZEB2 in mouse and human somitogenesis. Overall, this study provides a rich resource for developmental and synthetic biology communities endeavoring to understand mammalian embryogenesis.
Collapse
Affiliation(s)
- Suzan Stelloo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands.
| | - Maria Teresa Alejo-Vinogradova
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Charlotte A G H van Gelder
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Dick W Zijlmans
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marek J van Oostrom
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Juan Manuel Valverde
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Lieke A Lamers
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Teja Rus
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Paula Sobrevals Alcaraz
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Tilman Schäfers
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Cristina Furlan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marijke P A Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Katharina F Sonnen
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Boudewijn Burgering
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Maarten A F M Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands; Division of Molecular Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
| |
Collapse
|
2
|
Wang C, De Francesco R, Lamers LA, Rinzema S, Frölich S, van Lent PLEM, Logie C, van den Bosch MHJ. Transcriptomic profiling of osteoarthritis synovial macrophages reveals a tolerized phenotype compounded by a weak corticosteroid response. Rheumatology (Oxford) 2024:keae161. [PMID: 38466933 DOI: 10.1093/rheumatology/keae161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 01/09/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024] Open
Abstract
OBJECTIVES It is well-known that long-term osteoarthritis prognosis is not improved by corticosteroid treatments. Here we investigate what could underlie this phenomenon by measuring the short term corticosteroid response of OA-Mf. METHODS We determined the genome-wide transcriptomic response to corticosteroids of end-stage osteoarthritic joint synovial macrophages (OA-Mf). This was compared with LPS-tolerized and β-glucan-trained circulating blood monocyte-derived macrophage models. RESULTS Upon corticosteroid stimulation, the trained and tolerized macrophages significantly alter the abundance of 201 and 257 RNA transcripts, respectively. By contrast, by the same criteria, OA-Mf have a very restricted corticosteroid response of only 12 RNA transcripts. Furthermore, while metalloproteinases 1, -2, -3 and -10 expression clearly distinguish OA-Mf from both the tolerized and trained macrophage models, OA-Mf Interleukin 1 (IL1), chemokine (CXCL) and cytokine (CCL) family member profiles resemble the tolerized macrophage model, with the exception that OA-Mf show high levels of CCL20. CONCLUSION Terminal osteoarthritis joints therefore harbor macrophages with an inflammatory state that closely resembles the tolerized macrophage state and this is compounded by a weak corticosteroid response capacity that may explain the lack of positive long-term effects of corticosteroid treatment for osteoarthritis patients.
Collapse
Affiliation(s)
- Cheng Wang
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Ruben De Francesco
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Experimental Rheumatology, Department of Rheumatology, Radboud university medical center, Nijmegen, the Netherlands
| | - Lieke A Lamers
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Sybren Rinzema
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Siebren Frölich
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Peter L E M van Lent
- Experimental Rheumatology, Department of Rheumatology, Radboud university medical center, Nijmegen, the Netherlands
| | - Colin Logie
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Martijn H J van den Bosch
- Experimental Rheumatology, Department of Rheumatology, Radboud university medical center, Nijmegen, the Netherlands
| |
Collapse
|
3
|
Neikes HK, Kliza KW, Gräwe C, Wester RA, Jansen PWTC, Lamers LA, Baltissen MP, van Heeringen SJ, Logie C, Teichmann SA, Lindeboom RGH, Vermeulen M. Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq. Nat Biotechnol 2023; 41:1801-1809. [PMID: 36973556 DOI: 10.1038/s41587-023-01715-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 02/16/2023] [Indexed: 03/29/2023]
Abstract
Transcription factor binding across the genome is regulated by DNA sequence and chromatin features. However, it is not yet possible to quantify the impact of chromatin context on transcription factor binding affinities. Here, we report a method called binding affinities to native chromatin by sequencing (BANC-seq) to determine absolute apparent binding affinities of transcription factors to native DNA across the genome. In BANC-seq, a concentration range of a tagged transcription factor is added to isolated nuclei. Concentration-dependent binding is then measured per sample to quantify apparent binding affinities across the genome. BANC-seq adds a quantitative dimension to transcription factor biology, which enables stratification of genomic targets based on transcription factor concentration and prediction of transcription factor binding sites under non-physiological conditions, such as disease-associated overexpression of (onco)genes. Notably, whereas consensus DNA binding motifs for transcription factors are important to establish high-affinity binding sites, these motifs are not always strictly required to generate nanomolar-affinity interactions in the genome.
Collapse
Affiliation(s)
- Hannah K Neikes
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Katarzyna W Kliza
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Roelof A Wester
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Lieke A Lamers
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Simon J van Heeringen
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Colin Logie
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | | | - Rik G H Lindeboom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands.
- The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| |
Collapse
|
4
|
Wester RA, van Voorthuijsen L, Neikes HK, Dijkstra JJ, Lamers LA, Frölich S, van der Sande M, Logie C, Lindeboom RG, Vermeulen M. Retinoic acid signaling drives differentiation toward the absorptive lineage in colorectal cancer. iScience 2021; 24:103444. [PMID: 34877501 PMCID: PMC8633980 DOI: 10.1016/j.isci.2021.103444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/18/2021] [Accepted: 11/11/2021] [Indexed: 01/15/2023] Open
Abstract
Retinoic acid (RA) signaling is an important and conserved pathway that regulates cellular proliferation and differentiation. Furthermore, perturbed RA signaling is implicated in cancer initiation and progression. However, the mechanisms by which RA signaling contributes to homeostasis, malignant transformation, and disease progression in the intestine remain incompletely understood. Here, we report, in agreement with previous findings, that activation of the Retinoic Acid Receptor and the Retinoid X Receptor results in enhanced transcription of enterocyte-specific genes in mouse small intestinal organoids. Conversely, inhibition of this pathway results in reduced expression of genes associated with the absorptive lineage. Strikingly, this latter effect is conserved in a human organoid model for colorectal cancer (CRC) progression. We further show that RXR motif accessibility depends on progression state of CRC organoids. Finally, we show that reduced RXR target gene expression correlates with worse CRC prognosis, implying RA signaling as a putative therapeutic target in CRC. RA signaling contributes to enterocyte differentiation in murine intestinal organoids Inhibition of RXR decreases enterocyte gene expression in colon cancer organoids Accessibility of RXR motifs correlates with RXRi susceptibility High expression of RA signaling targets correlates with higher CRC patient survival
Collapse
Affiliation(s)
- Roelof A. Wester
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Lisa van Voorthuijsen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Hannah K. Neikes
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Jelmer J. Dijkstra
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Lieke A. Lamers
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Siebren Frölich
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Maarten van der Sande
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Colin Logie
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Rik G.H. Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Corresponding author
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
- Corresponding author
| |
Collapse
|