1
|
Guan G, Luo C, Tang LH, Tang C. Modulating cell proliferation by asymmetric division: A conserved pattern in the early embryogenesis of nematode species. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001006. [PMID: 38505394 PMCID: PMC10949086 DOI: 10.17912/micropub.biology.001006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/24/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
In the early stage of the nematode Caenorhabditis elegans embryogenesis, the zygote divides asymmetrically into a symmetric fast lineage and an asymmetric slow lineage, producing 16 and 8 cells respectively almost at the same time, followed by the onset of gastrulation. It was recently reported that this cell division pattern is optimal for rapid cell proliferation. In this work, we compare the cell lineages of 9 nematode species, revealing that this pattern is conserved for >60 million years. It further suggests that such lineage design has an important functional role and it might speed up embryonic development in the nematode kingdom, not limited to C. elegans , and independent of the maternal-zygotic transition dynamics.
Collapse
Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University
- South Bay Interdisciplinary Science Center, Songshan Lake Materials Laboratory
- Department of Physics, Hong Kong Baptist University
- Current Address: Department of Systems Biology, Harvard Medical School
- Current Address: Department of Data Science, Dana-Farber Cancer Institute
| | - Ce Luo
- Center for Quantitative Biology, Peking University
| | - Lei-Han Tang
- South Bay Interdisciplinary Science Center, Songshan Lake Materials Laboratory
- Department of Physics, Hong Kong Baptist University
- Institute of Computational and Theoretical Studies, Hong Kong Baptist University
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University
| | - Chao Tang
- Center for Quantitative Biology, Peking University
- Peking-Tsinghua Center for Life Sciences, Peking University
- School of Physics, Peking University
| |
Collapse
|
2
|
Hauser M, Zirman A, Rak R, Nachman I. Challenges and opportunities in cell expansion for cultivated meat. Front Nutr 2024; 11:1315555. [PMID: 38385010 PMCID: PMC10879929 DOI: 10.3389/fnut.2024.1315555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
The cultivation of meat using in vitro grown animal stem cells offers a promising solution to pressing global concerns around climate change, ethical considerations, and public health. However, cultivated meat introduces an unprecedented necessity: the generation of mass scales of cellular biomaterial, achieved by fostering cell proliferation within bioreactors. Existing methods for in vitro cell proliferation encounter substantial challenges in terms of both scalability and economic viability. Within this perspective, we discuss the current landscape of cell proliferation optimization, focusing on approaches pertinent to cellular agriculture. We examine the mechanisms governing proliferation rates, while also addressing intrinsic and conditional rate limitations. Furthermore, we expound upon prospective strategies that could lead to a significant enhancement of the overall scalability and cost-efficiency of the cell proliferation phase within the cultivated meat production process. By exploring knowledge from basic cell cycle studies, pathological contexts and tissue engineering, we may identify innovative solutions toward optimizing cell expansion.
Collapse
Affiliation(s)
- Michelle Hauser
- The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Amit Zirman
- The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Institute for Animal Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Roni Rak
- Institute for Animal Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Iftach Nachman
- The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
3
|
Zhang S, Wu S, Yao R, Wei X, Ohlstein B, Guo Z. Eclosion muscles secrete ecdysteroids to initiate asymmetric intestinal stem cell division in Drosophila. Dev Cell 2024; 59:125-140.e12. [PMID: 38096823 DOI: 10.1016/j.devcel.2023.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/05/2023] [Accepted: 11/14/2023] [Indexed: 01/11/2024]
Abstract
During organ development, tissue stem cells first expand via symmetric divisions and then switch to asymmetric divisions to minimize the time to obtain a mature tissue. In the Drosophila midgut, intestinal stem cells switch their divisions from symmetric to asymmetric at midpupal development to produce enteroendocrine cells. However, the signals that initiate this switch are unknown. Here, we identify the signal as ecdysteroids. In the presence of ecdysone, EcR and Usp promote the expression of E93 to suppress Br expression, resulting in asymmetric divisions. Surprisingly, the primary source of pupal ecdysone is not from the prothoracic gland but from dorsal internal oblique muscles (DIOMs), a group of transient skeletal muscles that are required for eclosion. Genetic analysis shows that DIOMs secrete ecdysteroids during mTOR-mediated muscle remodeling. Our findings identify sequential endocrine and mechanical roles for skeletal muscle, which ensure the timely asymmetric divisions of intestinal stem cells.
Collapse
Affiliation(s)
- Song Zhang
- Department of Medical Genetics, School of Basic Medicine, Institute for Brain Research, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Song Wu
- Department of Medical Genetics, School of Basic Medicine, Institute for Brain Research, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ruining Yao
- Department of Medical Genetics, School of Basic Medicine, Institute for Brain Research, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xueying Wei
- Department of Medical Genetics, School of Basic Medicine, Institute for Brain Research, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Benjamin Ohlstein
- Children's Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zheng Guo
- Department of Medical Genetics, School of Basic Medicine, Institute for Brain Research, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
| |
Collapse
|
4
|
Montazid S, Bandyopadhyay S, Hart DW, Gao N, Johnson B, Thrumurthy SG, Penn DJ, Wernisch B, Bansal M, Altrock PM, Rost F, Gazinska P, Ziolkowski P, Hayee B, Liu Y, Han J, Tessitore A, Koth J, Bodmer WF, East JE, Bennett NC, Tomlinson I, Irshad S. Adult stem cell activity in naked mole rats for long-term tissue maintenance. Nat Commun 2023; 14:8484. [PMID: 38123565 PMCID: PMC10733326 DOI: 10.1038/s41467-023-44138-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
The naked mole rat (NMR), Heterocephalus glaber, the longest-living rodent, provides a unique opportunity to explore how evolution has shaped adult stem cell (ASC) activity and tissue function with increasing lifespan. Using cumulative BrdU labelling and a quantitative imaging approach to track intestinal ASCs (Lgr5+) in their native in vivo state, we find an expanded pool of Lgr5+ cells in NMRs, and these cells specifically at the crypt base (Lgr5+CBC) exhibit slower division rates compared to those in short-lived mice but have a similar turnover as human LGR5+CBC cells. Instead of entering quiescence (G0), NMR Lgr5+CBC cells reduce their division rates by prolonging arrest in the G1 and/or G2 phases of the cell cycle. Moreover, we also observe a higher proportion of differentiated cells in NMRs that confer enhanced protection and function to the intestinal mucosa which is able to detect any chemical imbalance in the luminal environment efficiently, triggering a robust pro-apoptotic, anti-proliferative response within the stem/progenitor cell zone.
Collapse
Affiliation(s)
- Shamir Montazid
- Nuffield Department of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Daniel W Hart
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, 0028, Republic of South Africa
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, 07102, NJ, USA
| | - Brian Johnson
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, 92093, CA, USA
| | - Sri G Thrumurthy
- Endoscopy, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Dustin J Penn
- Konrad Lorenz Institute of Ethology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine, Vienna, 1160, Austria
| | - Bettina Wernisch
- Konrad Lorenz Institute of Ethology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine, Vienna, 1160, Austria
| | | | - Philipp M Altrock
- Department for Theoretical Biology, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany
| | - Fabian Rost
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | - Patrycja Gazinska
- Biobank Research Group, Lukasiewicz Research Network, PORT Polish Center for Technology Development, Wroclaw, Poland
| | - Piotr Ziolkowski
- Department of Clinical and Experimental Pathology, Wroclaw Medical University, 50-368, Wroclaw, Poland
| | - Bu'Hussain Hayee
- Endoscopy, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Yue Liu
- Department of Biological Sciences, Rutgers University, Newark, 07102, NJ, USA
| | - Jiangmeng Han
- Department of Biological Sciences, Rutgers University, Newark, 07102, NJ, USA
| | | | - Jana Koth
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Walter F Bodmer
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - James E East
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Nigel C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, 0028, Republic of South Africa
| | - Ian Tomlinson
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Shazia Irshad
- Nuffield Department of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK.
| |
Collapse
|
5
|
Montes-Olivas S, Legge D, Lund A, Fletcher AG, Williams AC, Marucci L, Homer M. In-silico and in-vitro morphometric analysis of intestinal organoids. PLoS Comput Biol 2023; 19:e1011386. [PMID: 37578984 PMCID: PMC10473498 DOI: 10.1371/journal.pcbi.1011386] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 09/01/2023] [Accepted: 07/25/2023] [Indexed: 08/16/2023] Open
Abstract
Organoids offer a powerful model to study cellular self-organisation, the growth of specific tissue morphologies in-vitro, and to assess potential medical therapies. However, the intrinsic mechanisms of these systems are not entirely understood yet, which can result in variability of organoids due to differences in culture conditions and basement membrane extracts used. Improving the standardisation of organoid cultures is essential for their implementation in clinical protocols. Developing tools to assess and predict the behaviour of these systems may produce a more robust and standardised biological model to perform accurate clinical studies. Here, we developed an algorithm to automate crypt-like structure counting on intestinal organoids in both in-vitro and in-silico images. In addition, we modified an existing two-dimensional agent-based mathematical model of intestinal organoids to better describe the system physiology, and evaluated its ability to replicate budding structures compared to new experimental data we generated. The crypt-counting algorithm proved useful in approximating the average number of budding structures found in our in-vitro intestinal organoid culture images on days 3 and 7 after seeding. Our changes to the in-silico model maintain the potential to produce simulations that replicate the number of budding structures found on days 5 and 7 of in-vitro data. The present study aims to aid in quantifying key morphological structures and provide a method to compare both in-vitro and in-silico experiments. Our results could be extended later to 3D in-silico models.
Collapse
Affiliation(s)
- Sandra Montes-Olivas
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Danny Legge
- Colorectal Tumour Biology Group, School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Abbie Lund
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Alexander G. Fletcher
- School of Mathematics and Statistics, University of Sheffield, Sheffield, United Kingdom
- Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Ann C. Williams
- Colorectal Tumour Biology Group, School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- BrisSynBio, Bristol, United Kingdom
| | - Martin Homer
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
6
|
Rocha-Martins M, Nerli E, Kretzschmar J, Weigert M, Icha J, Myers EW, Norden C. Neuronal migration prevents spatial competition in retinal morphogenesis. Nature 2023; 620:615-624. [PMID: 37558872 DOI: 10.1038/s41586-023-06392-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/30/2023] [Indexed: 08/11/2023]
Abstract
The concomitant occurrence of tissue growth and organization is a hallmark of organismal development1-3. This often means that proliferating and differentiating cells are found at the same time in a continuously changing tissue environment. How cells adapt to architectural changes to prevent spatial interference remains unclear. Here, to understand how cell movements that are key for growth and organization are orchestrated, we study the emergence of photoreceptor neurons that occur during the peak of retinal growth, using zebrafish, human tissue and human organoids. Quantitative imaging reveals that successful retinal morphogenesis depends on the active bidirectional translocation of photoreceptors, leading to a transient transfer of the entire cell population away from the apical proliferative zone. This pattern of migration is driven by cytoskeletal machineries that differ depending on the direction: microtubules are exclusively required for basal translocation, whereas actomyosin is involved in apical movement. Blocking the basal translocation of photoreceptors induces apical congestion, which hampers the apical divisions of progenitor cells and leads to secondary defects in lamination. Thus, photoreceptor migration is crucial to prevent competition for space, and to allow concurrent tissue growth and lamination. This shows that neuronal migration, in addition to its canonical role in cell positioning4, can be involved in coordinating morphogenesis.
Collapse
Affiliation(s)
- Mauricio Rocha-Martins
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden (CSBD), Dresden, Germany.
| | - Elisa Nerli
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden (CSBD), Dresden, Germany
| | - Jenny Kretzschmar
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Martin Weigert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden (CSBD), Dresden, Germany
- Institute of Bioengineering, School of Life Sciences École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jaroslav Icha
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden (CSBD), Dresden, Germany
| | - Caren Norden
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| |
Collapse
|
7
|
McCarthy N, Tie G, Madha S, He R, Kraiczy J, Maglieri A, Shivdasani RA. Smooth muscle contributes to the development and function of a layered intestinal stem cell niche. Dev Cell 2023; 58:550-564.e6. [PMID: 36924771 PMCID: PMC10089980 DOI: 10.1016/j.devcel.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 12/05/2022] [Accepted: 02/20/2023] [Indexed: 03/17/2023]
Abstract
Wnt and Rspondin (RSPO) signaling drives proliferation, and bone morphogenetic protein inhibitors (BMPi) impede differentiation, of intestinal stem cells (ISCs). Here, we identify the mouse ISC niche as a complex, multi-layered structure that encompasses distinct mesenchymal and smooth muscle populations. In young and adult mice, diverse sub-cryptal cells provide redundant ISC-supportive factors; few of these are restricted to single cell types. Niche functions refine during postnatal crypt morphogenesis, in part to oppose the dense aggregation of differentiation-promoting BMP+ sub-epithelial myofibroblasts at crypt-villus junctions. Muscularis mucosae, a specialized muscle layer, first appears during this period and supplements neighboring RSPO and BMPi sources. Components of this developing niche are conserved in human fetuses. The in vivo ablation of mouse postnatal smooth muscle increases BMP signaling activity, potently limiting a pre-weaning burst of crypt fission. Thus, distinct and progressively specialized mesenchymal cells together create the milieu that is required to propagate crypts during rapid organ growth and to sustain adult ISCs.
Collapse
Affiliation(s)
- Neil McCarthy
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Guodong Tie
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shariq Madha
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ruiyang He
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Judith Kraiczy
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Adrianna Maglieri
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA.
| |
Collapse
|
8
|
Rules for body fat interventions based on an operating point mechanism. iScience 2023; 26:106047. [PMID: 36818281 PMCID: PMC9929596 DOI: 10.1016/j.isci.2023.106047] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/15/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Interventions to reduce fat are important for human health. However, they can have opposing effects such as exercise that decreases fat but increases food intake, or coherent effects such as leptin resistance which raises both. Furthermore, some interventions show an overshoot in food intake, such as recovery from a diet, whereas others do not. To explain these properties we present a graphical framework called the operating point model, based on leptin control of feeding behavior. Steady-state fat and food intake is given by the intersection of two experimental curves - steady-state fat at a given food intake and ad libitum food intake at a given fat level. Depending on which curve an intervention shifts, it has opposing or coherent effects with or without overshoot, in excellent agreement with rodent data. The model also explains the quadratic relation between leptin and fat in humans. These concepts may guide the understanding of fat regulation disorders.
Collapse
|
9
|
Guevara-Garcia A, Soleilhac M, Minc N, Delacour D. Regulation and functions of cell division in the intestinal tissue. Semin Cell Dev Biol 2023:S1084-9521(23)00004-6. [PMID: 36702722 DOI: 10.1016/j.semcdb.2023.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/16/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023]
Abstract
In multicellular organisms, epithelial cells are key elements of tissue organization. In developing epithelial tissues, cellular proliferation and differentiation are under the tight regulation of morphogenetic programs to ensure correct organ formation and functioning. In these processes, proliferation rates and division orientation regulate the speed, timing and direction of tissue expansion but also its proper patterning. Moreover, tissue homeostasis relies on spatio-temporal modulations of daughter cell behavior and arrangement. These aspects are particularly crucial in the intestine, which is one of the most proliferative tissues in adults, making it a very attractive adult organ system to study the role of cell division on epithelial morphogenesis and organ function. Although epithelial cell division has been the subject of intense research for many years in multiple models, it still remains in its infancy in the context of the intestinal tissue. In this review, we focus on the current knowledge on cell division and regulatory mechanisms at play in the intestinal epithelial tissue, as well as their importance in developmental biology and physiopathology.
Collapse
Affiliation(s)
| | - Matis Soleilhac
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France
| | - Nicolas Minc
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France
| | - Delphine Delacour
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France.
| |
Collapse
|
10
|
Wang S, Garcia-Ojalvo J, Elowitz MB. Periodic spatial patterning with a single morphogen. Cell Syst 2022; 13:1033-1047.e7. [PMID: 36435178 DOI: 10.1016/j.cels.2022.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/13/2022] [Accepted: 11/02/2022] [Indexed: 11/26/2022]
Abstract
During multicellular development, periodic spatial patterning systems generate repetitive structures, such as digits, vertebrae, and teeth. Turing patterning provides a foundational paradigm for understanding such systems. The simplest Turing systems are believed to require at least two morphogens to generate periodic patterns. Here, using mathematical modeling, we show that a simpler circuit, including only a single diffusible morphogen, is sufficient to generate long-range, spatially periodic patterns that propagate outward from transient initiating perturbations and remain stable after the perturbation is removed. Furthermore, an additional bistable intracellular feedback or operation on a growing cell lattice can make patterning robust to noise. Together, these results show that a single morphogen can be sufficient for robust spatial pattern formation and should provide a foundation for engineering pattern formation in the emerging field of synthetic developmental biology.
Collapse
Affiliation(s)
- Sheng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
| |
Collapse
|
11
|
Corominas-Murtra B, Hannezo E. Modelling the dynamics of mammalian gut homeostasis. Semin Cell Dev Biol 2022:S1084-9521(22)00317-2. [DOI: 10.1016/j.semcdb.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/26/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
|
12
|
Huelsz-Prince G, Kok RNU, Goos Y, Bruens L, Zheng X, Ellenbroek S, Van Rheenen J, Tans S, van Zon JS. Mother cells control daughter cell proliferation in intestinal organoids to minimize proliferation fluctuations. eLife 2022; 11:80682. [PMID: 36445322 PMCID: PMC9708068 DOI: 10.7554/elife.80682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/20/2022] [Indexed: 11/30/2022] Open
Abstract
During renewal of the intestine, cells are continuously generated by proliferation. Proliferation and differentiation must be tightly balanced, as any bias toward proliferation results in uncontrolled exponential growth. Yet, the inherently stochastic nature of cells raises the question how such fluctuations are limited. We used time-lapse microscopy to track all cells in crypts of growing mouse intestinal organoids for multiple generations, allowing full reconstruction of the underlying lineage dynamics in space and time. Proliferative behavior was highly symmetric between sister cells, with both sisters either jointly ceasing or continuing proliferation. Simulations revealed that such symmetric proliferative behavior minimizes cell number fluctuations, explaining our observation that proliferating cell number remained constant even as crypts increased in size considerably. Proliferative symmetry did not reflect positional symmetry but rather lineage control through the mother cell. Our results indicate a concrete mechanism to balance proliferation and differentiation with minimal fluctuations that may be broadly relevant for other tissues.
Collapse
Affiliation(s)
| | | | | | - Lotte Bruens
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amterdam, Netherlands
| | - Xuan Zheng
- AMOLF, Science Park, Amsterdam, Netherlands
| | - Saskia Ellenbroek
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amterdam, Netherlands
| | - Jacco Van Rheenen
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amterdam, Netherlands
| | | | | |
Collapse
|
13
|
Fischer MM, Herzel H, Blüthgen N. Mathematical modelling identifies conditions for maintaining and escaping feedback control in the intestinal epithelium. Sci Rep 2022; 12:5569. [PMID: 35368028 PMCID: PMC8976856 DOI: 10.1038/s41598-022-09202-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/17/2022] [Indexed: 02/07/2023] Open
Abstract
The intestinal epithelium is one of the fastest renewing tissues in mammals. It shows a hierarchical organisation, where intestinal stem cells at the base of crypts give rise to rapidly dividing transit amplifying cells that in turn renew the pool of short-lived differentiated cells. Upon injury and stem-cell loss, cells can also de-differentiate. Tissue homeostasis requires a tightly regulated balance of differentiation and stem cell proliferation, and failure can lead to tissue extinction or to unbounded growth and cancerous lesions. Here, we present a two-compartment mathematical model of intestinal epithelium population dynamics that includes a known feedback inhibition of stem cell differentiation by differentiated cells. The model shows that feedback regulation stabilises the number of differentiated cells as these become invariant to changes in their apoptosis rate. Stability of the system is largely independent of feedback strength and shape, but specific thresholds exist which if bypassed cause unbounded growth. When dedifferentiation is added to the model, we find that the system can recover faster after certain external perturbations. However, dedifferentiation makes the system more prone to losing homeostasis. Taken together, our mathematical model shows how a feedback-controlled hierarchical tissue can maintain homeostasis and can be robust to many external perturbations.
Collapse
Affiliation(s)
- Matthias M Fischer
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin and Humboldt Universität zu Berlin, Berlin, 10115, Germany
- Institute of Pathology, Charité Universitätsmedizin Berlinn, Berlin, 10117, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin and Humboldt Universität zu Berlin, Berlin, 10115, Germany
| | - Nils Blüthgen
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin and Humboldt Universität zu Berlin, Berlin, 10115, Germany.
- Institute of Pathology, Charité Universitätsmedizin Berlinn, Berlin, 10117, Germany.
| |
Collapse
|
14
|
Davis JR, Ainslie AP, Williamson JJ, Ferreira A, Torres-Sánchez A, Hoppe A, Mangione F, Smith MB, Martin-Blanco E, Salbreux G, Tapon N. ECM degradation in the Drosophila abdominal epidermis initiates tissue growth that ceases with rapid cell-cycle exit. Curr Biol 2022; 32:1285-1300.e4. [PMID: 35167804 PMCID: PMC8967408 DOI: 10.1016/j.cub.2022.01.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 11/30/2021] [Accepted: 01/18/2022] [Indexed: 12/18/2022]
Abstract
During development, multicellular organisms undergo stereotypical patterns of tissue growth in space and time. How developmental growth is orchestrated remains unclear, largely due to the difficulty of observing and quantitating this process in a living organism. Drosophila histoblast nests are small clusters of progenitor epithelial cells that undergo extensive growth to give rise to the adult abdominal epidermis and are amenable to live imaging. Our quantitative analysis of histoblast proliferation and tissue mechanics reveals that tissue growth is driven by cell divisions initiated through basal extracellular matrix degradation by matrix metalloproteases secreted by the neighboring larval epidermal cells. Laser ablations and computational simulations show that tissue mechanical tension does not decrease as the histoblasts fill the abdominal epidermal surface. During tissue growth, the histoblasts display oscillatory cell division rates until growth termination occurs through the rapid emergence of G0/G1 arrested cells, rather than a gradual increase in cell-cycle time as observed in other systems such as the Drosophila wing and mouse postnatal epidermis. Different developing tissues can therefore achieve their final size using distinct growth termination strategies. Thus, adult abdominal epidermal development is characterized by changes in the tissue microenvironment and a rapid exit from the cell cycle.
Collapse
Affiliation(s)
- John Robert Davis
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Anna P Ainslie
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - John J Williamson
- Theoretical Physics of Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ana Ferreira
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Alejandro Torres-Sánchez
- Theoretical Physics of Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andreas Hoppe
- Faculty of Science, Engineering and Computing, Kingston University, Kingston-upon-Thames KT1 2EE, UK
| | - Federica Mangione
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Matthew B Smith
- Theoretical Physics of Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Enrique Martin-Blanco
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Parc Científic de Barcelona, C/Baldiri Reixac, 4-8, Torre R, 3era Planta, 08028 Barcelona, Spain
| | - Guillaume Salbreux
- Theoretical Physics of Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Genetics and Evolution, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland.
| | - Nicolas Tapon
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| |
Collapse
|
15
|
Dabelow S, LeHanka A, Jilkine A. Distinguishing between multiple mathematical models of neural stem cell quiescence and activation during age-related neural stem cell decline in neurogenesis. Math Biosci 2022; 346:108807. [PMID: 35304227 DOI: 10.1016/j.mbs.2022.108807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 02/16/2022] [Accepted: 03/05/2022] [Indexed: 10/18/2022]
Abstract
Stem cells are required for tissue maintenance and homeostasis during an organism's lifetime. Neural stem cells (NSCs) can be in an actively dividing state or in a quiescent state. The balance between stem cell quiescence and cycling activity determines the rate of neurogenesis. With age, more NSCs enter the quiescent state, while the total number of NSCs decreases. Here we reconsider an existing mathematical model of how neural stem cells switch between active and quiescent states from the point of view of control theory by considering the activation rate, self-renewal probability, and division rate as control parameters rather than as pre-defined functions. Our goal is to test whether those modifications to the basic model could explain the observed decline of neural stem cells with age better than Gomerzian time-dependent parameters, and compare the output from different model variants to experimental data from mice using AIC. We find that time-dependent activation rate provides the best fit to the activated cell fraction (ACF) of NSCs over time, but that other model variants with constant parameter values can better fit the total number of NSCs over time. We also consider an alternate model for NSCs with nonlinear feedback from progenitor cells that affect NSC parameters, and compare all models to experimental stem cell and progenitor data. However, all of the feedback models considered provide a worse fit to the experimental data. This suggests that when switching between active and quiescent stem cells is considered, a time-dependent linear model outperforms the integral feedback mechanism considered by other models of stem cell lineages. Fitting progenitor data for both the time varying models and feedback models indicates that four or five intermediate transit amplifying progenitor states are necessary. Our modeling suggests that in order to determine whether an increase in age-related neural stem cell quiescence is determined by by a decreasing stem cell activation rate or an increased stem cell depletion rate, additional experiments should be designed to explore whether or not depletion of the stem cell pool is occurring, and that a higher resolution time series for activated cell fraction (ACF) would be best to resolve this issue.
Collapse
|
16
|
Correa KDP, Silva MET, Ribeiro OS, Matta SLP, Peluzio MDCG, Oliveira EB, Coimbra JSDR. Homogenised and pasteurised human milk: lipid profile and effect as a supplement in the enteral diet of Wistar rats. Br J Nutr 2022; 127:711-721. [PMID: 33902762 DOI: 10.1017/s0007114521001380] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The retention of human milk (HM) fat in nasogastric probes of infusion pumps can be observed during the feed of infants unable to suck at the mother's breast. The lack of homogenisation of HM could contribute to the fat holding. Therefore, the present study evaluated (i) the influence of homogenisation on milk fat retaining in infant feeding probes and (ii) the in vivo effect of the homogenisation on lipid absorption by Wistar rats. The animals were fed with HM treated following two processing conditions, that is, pasteurised and homogenised-pasteurised. The animals were randomly subdivided into four experimental groups: water-fed (control), pasteurised milk, homogenised-pasteurised milk and pasteurised-skimmed milk. The results of food consumption, mass body gain, corporate metrics and plasma blood levels of total cholesterol did not show any difference (P < 0·05) among the three types of HM used in the experiments. The liver, intestine and intra-abdominal adipose tissue of the four groups of animals presented normal and healthy histology. The composition of fatty acids in the brain tissue of animals fed with homogenised HM increased when compared with the groups fed with non-homogenised HM. These values were 11·08 % higher for arachidonic acids, 6·59 % for DAH and 47·92 % for nervous acids. The ingestion of homogenised HM promoted higher absorption of milk nutrients. Therefore, the addition of the homogenisation stage in HM processing could be an alternative to reduce fat retention in probes and to improve the lipids' absorption in the body.
Collapse
Affiliation(s)
- Kely de Paula Correa
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa (UFV), Av. P.H. Rolfs, s/n, 36570-900 Viçosa, MG, Brasil
| | - Monique E T Silva
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa (UFV), Av. P.H. Rolfs, s/n, 36570-900 Viçosa, MG, Brasil
| | - Otávio S Ribeiro
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa (UFV), Av. P.H. Rolfs, s/n, 36570-900 Viçosa, MG, Brasil
| | - Sérgio L P Matta
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa (UFV), Av. P.H. Rolfs, s/n, 36570-900 Viçosa, MG, Brasil
| | - Maria do Carmo G Peluzio
- Departamento de Nutrição e Saúde, Universidade Federal de Viçosa (UFV), Av. P.H. Rolfs, s/n, 36570-900 Viçosa, MG, Brasil
| | - Eduardo B Oliveira
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa (UFV), Av. P.H. Rolfs, s/n, 36570-900 Viçosa, MG, Brasil
| | - Jane S Dos R Coimbra
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa (UFV), Av. P.H. Rolfs, s/n, 36570-900 Viçosa, MG, Brasil
| |
Collapse
|
17
|
Sun X, Xue Z, Yasin A, He Y, Chai Y, Li J, Zhang K. Colorectal Cancer and Adjacent Normal Mucosa Differ in Apoptotic and Inflammatory Protein Expression. ENGINEERED REGENERATION 2022. [DOI: 10.1016/j.engreg.2022.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
|
18
|
Guan G, Wong MK, Zhao Z, Tang LH, Tang C. Volume segregation programming in a nematode's early embryogenesis. Phys Rev E 2021; 104:054409. [PMID: 34942757 DOI: 10.1103/physreve.104.054409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/15/2021] [Indexed: 11/07/2022]
Abstract
Nematode species are well-known for their invariant cell lineage pattern during development. Combining knowledge about the fate specification induced by asymmetric division and the anti-correlation between cell cycle length and cell volume in Caenorhabditis elegans, we propose a minimal model to simulate lineage initiation by altering cell volume segregation ratio in each division, and quantify the derived pattern's performance in proliferation speed, fate diversity, and space robustness. The stereotypic pattern in C. elegans embryo is found to be one of the most optimal solutions taking minimum time to achieve the cell number before gastrulation, by programming asymmetric divisions as a strategy.
Collapse
Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Ming-Kin Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.,State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Lei-Han Tang
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.,Department of Physics and Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Hong Kong, China.,Complex Systems Division, Beijing Computational Science Research Center, Beijing 100094, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China
| |
Collapse
|
19
|
Ono H, Arai Y, Furukawa E, Narushima D, Matsuura T, Nakamura H, Shiokawa D, Nagai M, Imai T, Mimori K, Okamoto K, Hippo Y, Shibata T, Kato M. Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model. BMC Biol 2021; 19:207. [PMID: 34548081 PMCID: PMC8456589 DOI: 10.1186/s12915-021-01147-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/06/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Intra-tumor heterogeneity (ITH) encompasses cellular differences in tumors and is related to clinical outcomes such as drug resistance. However, little is known about the dynamics of ITH, owing to the lack of time-series analysis at the single-cell level. Mouse models that recapitulate cancer development are useful for controlled serial time sampling. RESULTS We performed single-cell exome and transcriptome sequencing of 200 cells to investigate how ITH is generated in a mouse colorectal cancer model. In the model, a single normal intestinal cell is grown into organoids that mimic the intestinal crypt structure. Upon RNAi-mediated downregulation of a tumor suppressor gene APC, the transduced organoids were serially transplanted into mice to allow exposure to in vivo microenvironments, which play relevant roles in cancer development. The ITH of the transcriptome increased after the transplantation, while that of the exome decreased. Mutations generated during organoid culture did not greatly change at the bulk-cell level upon the transplantation. The RNA ITH increase was due to the emergence of new transcriptional subpopulations. In contrast to the initial cells expressing mesenchymal-marker genes, new subpopulations repressed these genes after the transplantation. Analyses of colorectal cancer data from The Cancer Genome Atlas revealed a high proportion of metastatic cases in human subjects with expression patterns similar to the new cell subpopulations in mouse. These results suggest that the birth of transcriptional subpopulations may be a key for adaptation to drastic micro-environmental changes when cancer cells have sufficient genetic alterations at later tumor stages. CONCLUSIONS This study revealed an evolutionary dynamics of single-cell RNA and DNA heterogeneity in tumor progression, giving insights into the mesenchymal-epithelial transformation of tumor cells at metastasis in colorectal cancer.
Collapse
Affiliation(s)
- Hanako Ono
- Division of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Eisaku Furukawa
- Division of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Daichi Narushima
- Division of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tetsuya Matsuura
- Department of Animal Experimentation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Daisuke Shiokawa
- Division of Cancer Differentiation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Momoko Nagai
- Division of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Toshio Imai
- Department of Animal Experimentation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, 101 Hasamamachiidaigaoka, Yufu, Oita, 879-5593, Japan
| | - Koji Okamoto
- Division of Cancer Differentiation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yoshitaka Hippo
- Department of Animal Experimentation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Division of Biochemistry and Molecular Carcinogenesis, Chiba Cancer Center Research Institute, 666-2 Nitona-cho, Chiba Chuo-ku, Chiba, 260-8717, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shiroganedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Mamoru Kato
- Division of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| |
Collapse
|
20
|
Sprangers J, Zaalberg IC, Maurice MM. Organoid-based modeling of intestinal development, regeneration, and repair. Cell Death Differ 2021; 28:95-107. [PMID: 33208888 PMCID: PMC7852609 DOI: 10.1038/s41418-020-00665-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
The intestinal epithelium harbors a remarkable adaptability to undergo injury-induced repair. A key part of the regenerative response is the transient reprogramming of epithelial cells into a fetal-like state, which drives uniform proliferation, tissue remodeling, and subsequent restoration of the homeostatic state. In this review, we discuss how Wnt and YAP signaling pathways control the intestinal repair response and the transitioning of cell states, in comparison with the process of intestinal development. Furthermore, we highlight how organoid-based applications have contributed to the characterization of the mechanistic principles and key players that guide these developmental and regenerative events.
Collapse
Affiliation(s)
- Joep Sprangers
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Irene C Zaalberg
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Madelon M Maurice
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| |
Collapse
|
21
|
Tsiantis N, Banga JR. Using optimal control to understand complex metabolic pathways. BMC Bioinformatics 2020; 21:472. [PMID: 33087041 PMCID: PMC7579911 DOI: 10.1186/s12859-020-03808-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Optimality principles have been used to explain the structure and behavior of living matter at different levels of organization, from basic phenomena at the molecular level, up to complex dynamics in whole populations. Most of these studies have assumed a single-criteria approach. Such optimality principles have been justified from an evolutionary perspective. In the context of the cell, previous studies have shown how dynamics of gene expression in small metabolic models can be explained assuming that cells have developed optimal adaptation strategies. Most of these works have considered rather simplified representations, such as small linear pathways, or reduced networks with a single branching point, and a single objective for the optimality criteria. RESULTS Here we consider the extension of this approach to more realistic scenarios, i.e. biochemical pathways of arbitrary size and structure. We first show that exploiting optimality principles for these networks poses great challenges due to the complexity of the associated optimal control problems. Second, in order to surmount such challenges, we present a computational framework which has been designed with scalability and efficiency in mind, including mechanisms to avoid the most common pitfalls. Third, we illustrate its performance with several case studies considering the central carbon metabolism of S. cerevisiae and B. subtilis. In particular, we consider metabolic dynamics during nutrient shift experiments. CONCLUSIONS We show how multi-objective optimal control can be used to predict temporal profiles of enzyme activation and metabolite concentrations in complex metabolic pathways. Further, we also show how to consider general cost/benefit trade-offs. In this study we have considered metabolic pathways, but this computational framework can also be applied to analyze the dynamics of other complex pathways, such as signal transduction or gene regulatory networks.
Collapse
Affiliation(s)
- Nikolaos Tsiantis
- Bioprocess Engineering Group, Spanish National Research Council, IIM-CSIC, C/Eduardo Cabello 6, 36208 Vigo, Spain
- Department of Chemical Engineering, University of Vigo, 36310 Vigo, Spain
| | - Julio R. Banga
- Bioprocess Engineering Group, Spanish National Research Council, IIM-CSIC, C/Eduardo Cabello 6, 36208 Vigo, Spain
| |
Collapse
|
22
|
Sei Y, Feng J, Zhao X, Wank SA. Role of an active reserve stem cell subset of enteroendocrine cells in intestinal stem cell dynamics and the genesis of small intestinal neuroendocrine tumors. Am J Physiol Gastrointest Liver Physiol 2020; 319:G494-G501. [PMID: 32845170 PMCID: PMC7654644 DOI: 10.1152/ajpgi.00278.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Small intestinal neuroendocrine tumors (SI-NET) are serotonin-secreting well-differentiated neuroendocrine tumors of putative enterochromaffin (EC) cell origin. Recent studies recognize a subset of EC cells that is label-retaining at the +4 position in the crypt and functions as a reserve intestinal stem cell. Importantly, this +4 reserve EC cell subset not only contributes to regeneration of the intestinal epithelium during injury and inflammation but also to basal crypt homeostasis at a constant rate. The latter function suggests that the +4 EC cell subset serves as an active reserve stem cell via a constant rate of dedifferentiation. Characterization of early tumor formation of SI-NET, observed as crypt-based EC cell clusters in many cases of familial SI-NETs, suggests that the +4 active reserve EC cell subset is the cell of origin. This newly discovered active reserve stem cell property of EC cells can account for unique biological mechanisms and processes associated with the genesis and development of SI-NETs. The recognition of this property of the +4 active reserve EC cell subset may provide novel opportunities to explore NETs in the gastrointestinal tract and other organs.
Collapse
Affiliation(s)
- Yoshitatsu Sei
- Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jianying Feng
- Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Xilin Zhao
- Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Stephen A. Wank
- Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
23
|
p53 drives a transcriptional program that elicits a non-cell-autonomous response and alters cell state in vivo. Proc Natl Acad Sci U S A 2020; 117:23663-23673. [PMID: 32900967 DOI: 10.1073/pnas.2008474117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cell stress and DNA damage activate the tumor suppressor p53, triggering transcriptional activation of a myriad of target genes. The molecular, morphological, and physiological consequences of this activation remain poorly understood in vivo. We activated a p53 transcriptional program in mice by deletion of Mdm2, a gene that encodes the major p53 inhibitor. By overlaying tissue-specific RNA-sequencing data from pancreas, small intestine, ovary, kidney, and heart with existing p53 chromatin immunoprecipitation (ChIP) sequencing, we identified a large repertoire of tissue-specific p53 genes and a common p53 transcriptional signature of seven genes, which included Mdm2 but not p21 Global p53 activation caused a metaplastic phenotype in the pancreas that was missing in mice with acinar-specific p53 activation, suggesting non-cell-autonomous effects. The p53 cellular response at single-cell resolution in the intestine altered transcriptional cell state, leading to a proximal enterocyte population enriched for genes within oxidative phosphorylation pathways. In addition, a population of active CD8+ T cells was recruited. Combined, this study provides a comprehensive profile of the p53 transcriptional response in vivo, revealing both tissue-specific transcriptomes and a unique signature, which were integrated to induce both cell-autonomous and non-cell-autonomous responses and transcriptional plasticity.
Collapse
|
24
|
Joly A, Rousset R. Tissue Adaptation to Environmental Cues by Symmetric and Asymmetric Division Modes of Intestinal Stem Cells. Int J Mol Sci 2020; 21:ijms21176362. [PMID: 32887329 PMCID: PMC7504256 DOI: 10.3390/ijms21176362] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/28/2020] [Accepted: 08/30/2020] [Indexed: 12/20/2022] Open
Abstract
Tissues must adapt to the different external stimuli so that organisms can survive in their environments. The intestine is a vital organ involved in food processing and absorption, as well as in innate immune response. Its adaptation to environmental cues such as diet and biotic/abiotic stress involves regulation of the proliferative rate and a switch of division mode (asymmetric versus symmetric) of intestinal stem cells (ISC). In this review, we outline the current comprehension of the physiological and molecular mechanisms implicated in stem cell division modes in the adult Drosophila midgut. We present the signaling pathways and polarity cues that control the mitotic spindle orientation, which is the terminal determinant ensuring execution of the division mode. We review these events during gut homeostasis, as well as during its response to nutrient availability, bacterial infection, chemical damage, and aging. JNK signaling acts as a central player, being involved in each of these conditions as a direct regulator of spindle orientation. The studies of the mechanisms regulating ISC divisions allow a better understanding of how adult stem cells integrate different signals to control tissue plasticity, and of how various diseases, notably cancers, arise from their alterations.
Collapse
|
25
|
Dekoninck S, Hannezo E, Sifrim A, Miroshnikova YA, Aragona M, Malfait M, Gargouri S, de Neunheuser C, Dubois C, Voet T, Wickström SA, Simons BD, Blanpain C. Defining the Design Principles of Skin Epidermis Postnatal Growth. Cell 2020; 181:604-620.e22. [PMID: 32259486 PMCID: PMC7198979 DOI: 10.1016/j.cell.2020.03.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 02/10/2020] [Accepted: 03/05/2020] [Indexed: 11/20/2022]
Abstract
During embryonic and postnatal development, organs and tissues grow steadily to achieve their final size at the end of puberty. However, little is known about the cellular dynamics that mediate postnatal growth. By combining in vivo clonal lineage tracing, proliferation kinetics, single-cell transcriptomics, and in vitro micro-pattern experiments, we resolved the cellular dynamics taking place during postnatal skin epidermis expansion. Our data revealed that harmonious growth is engineered by a single population of developmental progenitors presenting a fixed fate imbalance of self-renewing divisions with an ever-decreasing proliferation rate. Single-cell RNA sequencing revealed that epidermal developmental progenitors form a more uniform population compared with adult stem and progenitor cells. Finally, we found that the spatial pattern of cell division orientation is dictated locally by the underlying collagen fiber orientation. Our results uncover a simple design principle of organ growth where progenitors and differentiated cells expand in harmony with their surrounding tissues.
Collapse
Affiliation(s)
- Sophie Dekoninck
- Université Libre de Bruxelles, Laboratory of Stem Cells and Cancer, Brussels 1070, Belgium
| | - Edouard Hannezo
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria; The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Alejandro Sifrim
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium; Wellcome Sanger Institute, Sanger Institute - EBI Single-Cell Genomics Centre, Hinxton, UK
| | - Yekaterina A Miroshnikova
- Helsinki Institute of Life Science, University of Helsinki, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland; Wihuri Research Institute, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland; Max Planck Institute for Biology of Ageing, Joseph Stelzmann Str. 9b, 50931 Cologne, Germany
| | - Mariaceleste Aragona
- Université Libre de Bruxelles, Laboratory of Stem Cells and Cancer, Brussels 1070, Belgium
| | - Milan Malfait
- Université Libre de Bruxelles, Laboratory of Stem Cells and Cancer, Brussels 1070, Belgium
| | - Souhir Gargouri
- Université Libre de Bruxelles, Laboratory of Stem Cells and Cancer, Brussels 1070, Belgium
| | | | - Christine Dubois
- Université Libre de Bruxelles, Laboratory of Stem Cells and Cancer, Brussels 1070, Belgium
| | - Thierry Voet
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium; Wellcome Sanger Institute, Sanger Institute - EBI Single-Cell Genomics Centre, Hinxton, UK
| | - Sara A Wickström
- Helsinki Institute of Life Science, University of Helsinki, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland; Wihuri Research Institute, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland; Max Planck Institute for Biology of Ageing, Joseph Stelzmann Str. 9b, 50931 Cologne, Germany
| | - Benjamin D Simons
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Cavendish Laboratory, Department of Physics, J. J. Thomson Avenue, Cambridge CB3 0HE, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, UK
| | - Cédric Blanpain
- Université Libre de Bruxelles, Laboratory of Stem Cells and Cancer, Brussels 1070, Belgium; WELBIO, Université Libre de Bruxelles, Brussels 1070, Belgium.
| |
Collapse
|
26
|
Pereira B, Amaral AL, Dias A, Mendes N, Muncan V, Silva AR, Thibert C, Radu AG, David L, Máximo V, van den Brink GR, Billaud M, Almeida R. MEX3A regulates Lgr5 + stem cell maintenance in the developing intestinal epithelium. EMBO Rep 2020; 21:e48938. [PMID: 32052574 PMCID: PMC7132344 DOI: 10.15252/embr.201948938] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
Intestinal stem cells (ISCs) fuel the lifelong self‐renewal of the intestinal tract and are paramount for epithelial repair. In this context, the Wnt pathway component LGR5 is the most consensual ISC marker to date. Still, the effort to better understand ISC identity and regulation remains a challenge. We have generated a Mex3a knockout mouse model and show that this RNA‐binding protein is crucial for the maintenance of the Lgr5+ISC pool, as its absence disrupts epithelial turnover during postnatal development and stereotypical organoid maturation ex vivo. Transcriptomic profiling of intestinal crypts reveals that Mex3a deletion induces the peroxisome proliferator‐activated receptor (PPAR) pathway, along with a decrease in Wnt signalling and loss of the Lgr5+ stem cell signature. Furthermore, we identify PPARγ activity as a molecular intermediate of MEX3A‐mediated regulation. We also show that high PPARγ signalling impairs Lgr5+ISC function, thus uncovering a new layer of post‐transcriptional regulation that critically contributes to intestinal homeostasis.
Collapse
Affiliation(s)
- Bruno Pereira
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Ana L Amaral
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Alexandre Dias
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Nuno Mendes
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Vanesa Muncan
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Tytgat Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Ana R Silva
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Chantal Thibert
- Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Anca G Radu
- Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Leonor David
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,FMUP-Faculty of Medicine, University of Porto, Porto, Portugal
| | - Valdemar Máximo
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,FMUP-Faculty of Medicine, University of Porto, Porto, Portugal
| | - Gijs R van den Brink
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Tytgat Institute, University of Amsterdam, Amsterdam, The Netherlands.,Medicines Research Center, GSK, Stevenage, UK
| | - Marc Billaud
- Clinical and Experimental Model of Lymphomagenesis, INSERM U1052, CNRS UMR5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Raquel Almeida
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,FMUP-Faculty of Medicine, University of Porto, Porto, Portugal.,Biology Department, Faculty of Sciences, University of Porto, Porto, Portugal
| |
Collapse
|
27
|
Das D, Fletcher RB, Ngai J. Cellular mechanisms of epithelial stem cell self-renewal and differentiation during homeostasis and repair. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2019; 9:e361. [PMID: 31468728 DOI: 10.1002/wdev.361] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 12/14/2022]
Abstract
Epithelia in adult mammals exhibit remarkable regenerative capacities owing to the presence of adult stem cells, which self-renew and differentiate to replace cells lost to normal turnover or injury. The mechanisms supporting tissue homeostasis and injury-induced repair often differ from each other as well as from those used in embryonic development. Recent studies have also highlighted the phenomenon of cellular plasticity in adult tissues, in which differentiated cells can change fate and even give rise to new stem cell populations to complement the canonical stem cells in promoting repair following injury. Signaling pathways such as WNT, bone morphogenetic protein, and Sonic Hedgehog play critical roles in stem cell maintenance and cell fate decisions across diverse epithelia and conditions, suggesting that conserved mechanisms underlie the regenerative capacity of adult epithelial structures. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Adult Stem Cells, Tissue Renewal, and Regeneration > Tissue Stem Cells and Niches Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cell Differentiation and Reversion Adult Stem Cells, Tissue Renewal, and Regeneration > Regeneration.
Collapse
Affiliation(s)
- Diya Das
- Department of Molecular and Cell Biology, University of California, Berkeley, California.,Berkeley Institute for Data Science, University of California, Berkeley, California
| | - Russell B Fletcher
- Department of Molecular and Cell Biology, University of California, Berkeley, California
| | - John Ngai
- Department of Molecular and Cell Biology, University of California, Berkeley, California.,Helen Wills Neuroscience Institute, University of California, Berkeley, California.,QB3 Functional Genomics Laboratory, University of California, Berkeley, California
| |
Collapse
|
28
|
Seishima R, Barker N. A contemporary snapshot of intestinal stem cells and their regulation. Differentiation 2019; 108:3-7. [DOI: 10.1016/j.diff.2019.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/15/2019] [Accepted: 01/24/2019] [Indexed: 01/10/2023]
|
29
|
Tracing the origin of adult intestinal stem cells. Nature 2019; 570:107-111. [PMID: 31092921 DOI: 10.1038/s41586-019-1212-5] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/15/2019] [Indexed: 12/14/2022]
Abstract
Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn, where they express markers such as LGR51,2 and fuel the constant replenishment of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise to adult intestinal stem cells3,4, it remains unclear whether this population in the patterned epithelium represents unique intestinal stem-cell precursors. Here we show, using unbiased quantitative lineage-tracing approaches, biophysical modelling and intestinal transplantation, that all cells of the mouse intestinal epithelium-irrespective of their location and pattern of LGR5 expression in the fetal gut tube-contribute actively to the adult intestinal stem cell pool. Using 3D imaging, we find that during fetal development the villus undergoes gross remodelling and fission. This brings epithelial cells from the non-proliferative villus into the proliferative intervillus region, which enables them to contribute to the adult stem-cell niche. Our results demonstrate that large-scale remodelling of the intestinal wall and cell-fate specification are closely linked. Moreover, these findings provide a direct link between the observed plasticity and cellular reprogramming of differentiating cells in adult tissues following damage5-9, revealing that stem-cell identity is an induced rather than a hardwired property.
Collapse
|
30
|
Alber AB, Suter DM. Dynamics of protein synthesis and degradation through the cell cycle. Cell Cycle 2019; 18:784-794. [PMID: 30907235 PMCID: PMC6527273 DOI: 10.1080/15384101.2019.1598725] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/18/2019] [Accepted: 03/12/2019] [Indexed: 01/05/2023] Open
Abstract
Protein expression levels depend on the balance between their synthesis and degradation rates. Even quiescent (G0) cells display a continuous turnover of proteins, despite protein levels remaining largely constant over time. In cycling cells, global protein levels need to be precisely doubled at each cell division in order to maintain cellular homeostasis, but we still lack a quantitative understanding of how this is achieved. Recent studies have shed light on cell cycle-dependent changes in protein synthesis and degradation rates. Here we discuss current population-based and single cell approaches used to assess protein synthesis and degradation, and review the insights they have provided into the dynamics of protein turnover in different cell cycle phases.
Collapse
Affiliation(s)
- Andrea Brigitta Alber
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - David Michael Suter
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| |
Collapse
|
31
|
Hartl L, Huelsz-Prince G, van Zon J, Tans SJ. Apical constriction is necessary for crypt formation in small intestinal organoids. Dev Biol 2019; 450:76-81. [PMID: 30914321 DOI: 10.1016/j.ydbio.2019.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 02/26/2019] [Accepted: 03/14/2019] [Indexed: 12/23/2022]
Abstract
Small intestinal organoids have become an important tool to study crypt homeostasis, cell fate dynamics and tissue biomechanics. Yet, the mechanisms that drive the budding of crypts from the smooth organoid epithelium remain incompletely understood. Locally enhanced proliferation has been suggested to induce tissue buckling and crypt initiation. Here we report that changes in cell morphology play a crucial role in crypt formation. Crypt formation is preceded by local epithelial thickening, apicobasal elongation, and apical narrowing, resulting in a wedge-like cell-shape, followed by apical evagination and crypt outgrowth. Myosin II activity is found to coincide with apical constriction of cells, while inhibition of myosin suppresses apical constriction and bud formation. The data suggest that myosin-driven apical constriction is a key driving force of bud initiation in small intestinal organoids.
Collapse
Affiliation(s)
- Leonie Hartl
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | | | - Jeroen van Zon
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | - Sander J Tans
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands.
| |
Collapse
|
32
|
Shakiba N, Fahmy A, Jayakumaran G, McGibbon S, David L, Trcka D, Elbaz J, Puri MC, Nagy A, van der Kooy D, Goyal S, Wrana JL, Zandstra PW. Cell competition during reprogramming gives rise to dominant clones. Science 2019; 364:science.aan0925. [DOI: 10.1126/science.aan0925] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 08/02/2018] [Accepted: 02/25/2019] [Indexed: 12/25/2022]
Abstract
The ability to generate induced pluripotent stem cells from differentiated cell types has enabled researchers to engineer cell states. Although studies have identified molecular networks that reprogram cells to pluripotency, the cellular dynamics of these processes remain poorly understood. Here, by combining cellular barcoding, mathematical modeling, and lineage tracing approaches, we demonstrate that reprogramming dynamics in heterogeneous populations are driven by dominant “elite” clones. Clones arise a priori from a population of poised mouse embryonic fibroblasts derived from Wnt1-expressing cells that may represent a neural crest–derived population. This work highlights the importance of cellular dynamics in fate programming outcomes and uncovers cell competition as a mechanism by which cells with eliteness emerge to occupy and dominate the reprogramming niche.
Collapse
|
33
|
Phillips NE, Mandic A, Omidi S, Naef F, Suter DM. Memory and relatedness of transcriptional activity in mammalian cell lineages. Nat Commun 2019; 10:1208. [PMID: 30872573 PMCID: PMC6418128 DOI: 10.1038/s41467-019-09189-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/21/2019] [Indexed: 12/03/2022] Open
Abstract
Phenotypically identical mammalian cells often display considerable variability in transcript levels of individual genes. How transcriptional activity propagates in cell lineages, and how this varies across genes is poorly understood. Here we combine live-cell imaging of short-lived transcriptional reporters in mouse embryonic stem cells with mathematical modelling to quantify the propagation of transcriptional activity over time and across cell generations in phenotypically homogenous cells. In sister cells we find mean transcriptional activity to be strongly correlated and transcriptional dynamics tend to be synchronous; both features control how quickly transcriptional levels in sister cells diverge in a gene-specific manner. Moreover, mean transcriptional activity is transmitted from mother to daughter cells, leading to multi-generational transcriptional memory and causing inter-family heterogeneity in gene expression.
Collapse
Affiliation(s)
- Nicholas E Phillips
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Aleksandra Mandic
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Saeed Omidi
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
| | - David M Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
| |
Collapse
|
34
|
Li J, Prochaska M, Maney L, Wallace KN. Development and organization of the zebrafish intestinal epithelial stem cell niche. Dev Dyn 2019; 249:76-87. [PMID: 30698914 DOI: 10.1002/dvdy.16] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 01/10/2019] [Accepted: 01/27/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Development of the vertebrate intestinal epithelial stem cell niche begins during embryogenesis but maturation occurs postembryonic. The intestinal mammalian crypt contains stem cells interspersed by secretory cells that play a role in regulation of proliferation. Epithelial cells are specified as either secretory or enterocytes as they migrate up the villi in mammals or fold in zebrafish. Zebrafish forms a functional intestine by the end of embryogenesis but takes another 4 weeks to develop the adult proliferation pattern. RESULTS We characterize development of the intestinal epithelial stem cell niche during the postembryonic period. During the first 2-weeks postembryogenesis, different groups of epithelial cells sequentially proceed through one or two cell cycles, appear to become quiescent, and remain at the interfold base. The third week begins asymmetric divisions with proliferative progeny moving up the folds. Apoptotic cells are not observed at the fold tip until the end of the fourth week. Secretory cells intersperse among interfold base proliferative cells, increasing in number during the third and fourth weeks with a coincident change in proliferation pattern. CONCLUSIONS Zebrafish postembryonic intestinal epithelial development consists of 2 weeks of slow proliferation followed by 2 weeks of metamorphosis to the adult structure. Developmental Dynamics 2019. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Jianlong Li
- Department of Biology, Clarkson University, Potsdam, New York
| | | | - Lea Maney
- Department of Biology, Clarkson University, Potsdam, New York
| | | |
Collapse
|
35
|
Sei Y, Feng J, Chow CC, Wank SA. Asymmetric cell division-dominant neutral drift model for normal intestinal stem cell homeostasis. Am J Physiol Gastrointest Liver Physiol 2019; 316:G64-G74. [PMID: 30359083 PMCID: PMC6383375 DOI: 10.1152/ajpgi.00242.2018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The normal intestinal epithelium is continuously regenerated at a rapid rate from actively cycling Lgr5-expressing intestinal stem cells (ISCs) that reside at the crypt base. Recent mathematical modeling based on several lineage-tracing studies in mice shows that the symmetric cell division-dominant neutral drift model fits well with the observed in vivo growth of ISC clones and suggests that symmetric divisions are central to ISC homeostasis. However, other studies suggest a critical role for asymmetric cell division in the maintenance of ISC homeostasis in vivo. Here, we show that the stochastic branching and Moran process models with both a symmetric and asymmetric division mode not only simulate the stochastic growth of the ISC clone in silico but also closely fit the in vivo stem cell dynamics observed in lineage-tracing studies. In addition, the proposed model with highest probability for asymmetric division is more consistent with in vivo observations reported here and by others. Our in vivo studies of mitotic spindle orientations and lineage-traced progeny pairs indicate that asymmetric cell division is a dominant mode used by ISCs under normal homeostasis. Therefore, we propose the asymmetric cell division-dominant neutral drift model for normal ISC homeostasis. NEW & NOTEWORTHY The prevailing mathematical model suggests that intestinal stem cells (ISCs) divide symmetrically. The present study provides evidence that asymmetric cell division is the major contributor to ISC maintenance and thus proposes an asymmetric cell division-dominant neutral drift model. Consistent with this model, in vivo studies of mitotic spindle orientation and lineage-traced progeny pairs indicate that asymmetric cell division is the dominant mode used by ISCs under normal homeostasis.
Collapse
Affiliation(s)
- Yoshitatsu Sei
- 1Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jianying Feng
- 1Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Carson C. Chow
- 2Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Stephen A. Wank
- 1Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
36
|
May AJ, Cruz-Pacheco N, Emmerson E, Gaylord EA, Seidel K, Nathan S, Muench MO, Klein OD, Knox SM. Diverse progenitor cells preserve salivary gland ductal architecture after radiation-induced damage. Development 2018; 145:dev.166363. [PMID: 30305288 DOI: 10.1242/dev.166363] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/02/2018] [Indexed: 12/11/2022]
Abstract
The ductal system of the salivary gland has long been postulated to be resistant to radiation-induced damage, a common side effect incurred by head and neck cancer patients receiving radiotherapy. Yet, whether the ducts are capable of regenerating after genotoxic injury, or whether damage to ductal cells induces lineage plasticity, as has been reported in other organ systems, remains unknown. Here, using the murine salivary gland, we show that two ductal progenitor populations, marked exclusively by KRT14 and KIT, maintain non-overlapping ductal compartments after radiation exposure but do so through distinct cellular mechanisms. KRT14+ progenitor cells are fast-cycling cells that proliferate in response to radiation-induced damage in a sustained manner and divide asymmetrically to produce differentiated cells of the larger granulated ducts. Conversely, KIT+ intercalated duct cells are long-lived progenitors for the intercalated ducts that undergo few cell divisions either during homeostasis or after gamma radiation, thus maintaining ductal architecture with slow rates of cell turnover. Together, these data illustrate the regenerative capacity of the salivary ducts and highlight the heterogeneity in the damage responses used by salivary progenitor cells to maintain tissue architecture.
Collapse
Affiliation(s)
- Alison J May
- Program in Craniofacial Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA.,Department of Cell and Tissue Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Noel Cruz-Pacheco
- Program in Craniofacial Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA.,Department of Cell and Tissue Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Elaine Emmerson
- Program in Craniofacial Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA.,Department of Cell and Tissue Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Eliza A Gaylord
- Program in Craniofacial Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA.,Department of Cell and Tissue Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Kerstin Seidel
- Program in Craniofacial Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA.,Department of Orofacial Sciences, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Sara Nathan
- Program in Craniofacial Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA.,Department of Cell and Tissue Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Marcus O Muench
- Blood Systems Research Institute, San Francisco, CA 94118, USA
| | - Ophir D Klein
- Program in Craniofacial Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA.,Department of Orofacial Sciences, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA.,Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sarah M Knox
- Program in Craniofacial Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA .,Department of Cell and Tissue Biology, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| |
Collapse
|
37
|
Cohen M, Giladi A, Gorki AD, Solodkin DG, Zada M, Hladik A, Miklosi A, Salame TM, Halpern KB, David E, Itzkovitz S, Harkany T, Knapp S, Amit I. Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting. Cell 2018; 175:1031-1044.e18. [DOI: 10.1016/j.cell.2018.09.009] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/16/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022]
|
38
|
Sei Y, Feng J, Samsel L, White A, Zhao X, Yun S, Citrin D, McCoy JP, Sundaresan S, Hayes MM, Merchant JL, Leiter A, Wank SA. Mature enteroendocrine cells contribute to basal and pathological stem cell dynamics in the small intestine. Am J Physiol Gastrointest Liver Physiol 2018; 315:G495-G510. [PMID: 29848020 PMCID: PMC6230697 DOI: 10.1152/ajpgi.00036.2018] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Lgr5-expressing intestinal stem cells (ISCs) maintain continuous and rapid generation of the intestinal epithelium. Here, we present evidence that dedifferentiation of committed enteroendocrine cells (EECs) contributes to maintenance of the epithelium under both basal conditions and in response to injury. Lineage-tracing studies identified a subset of EECs that reside at +4 position for more than 2 wk, most of which were BrdU-label-retaining cells. Under basal conditions, cells derived from these EECs grow from the bottom of the crypt to generate intestinal epithelium according to neutral drift kinetics that is consistent with dedifferentiation of mature EECs to ISCs. The lineage tracing of EECs demonstrated reserve stem cell properties in response to radiation-induced injury with the generation of reparative EEC-derived epithelial patches. Finally, the enterochromaffin (EC) cell was the predominant EEC type participating in these stem cell dynamics. These results provide novel insights into the +4 reserve ISC hypothesis, stem cell dynamics of the intestinal epithelium, and in the development of EC-derived small intestinal tumors. NEW & NOTEWORTHY The current manuscript demonstrating that a subset of mature enteroendocrine cells (EECs), predominantly enterochromaffin cells, dedifferentiates to fully functional intestinal stem cells (ISCs) is novel, timely, and important. These cells dedifferentiate to ISCs not only in response to injury but also under basal homeostatic conditions. These novel findings provide a mechanism in which a specified cell can dedifferentiate and contribute to normal tissue plasticity as well as the development of EEC-derived intestinal tumors under pathologic conditions.
Collapse
Affiliation(s)
- Yoshitatsu Sei
- 1Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jianying Feng
- 1Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Leigh Samsel
- 2Flow Cytometry Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Ayla White
- 3Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Xilin Zhao
- 1Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Sajung Yun
- 1Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Deborah Citrin
- 3Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - J. Philip McCoy
- 2Flow Cytometry Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Sinju Sundaresan
- 4Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, Michigan
| | - Michael M. Hayes
- 4Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, Michigan
| | - Juanita L. Merchant
- 5Department of Molecular and Integrative Physiology, University of Michigan Medical Center, Ann Arbor, Michigan
| | - Andrew Leiter
- 6Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Stephen A. Wank
- 1Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
39
|
Fornari C, O'Connor LO, Yates JWT, Cheung SYA, Jodrell DI, Mettetal JT, Collins TA. Understanding Hematological Toxicities Using Mathematical Modeling. Clin Pharmacol Ther 2018; 104:644-654. [PMID: 29604045 DOI: 10.1002/cpt.1080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/09/2018] [Accepted: 03/27/2018] [Indexed: 12/16/2022]
Abstract
Balancing antitumor efficacy with toxicity is a significant challenge, and drug-induced myelosuppression is a common dose-limiting toxicity of cancer treatments. Mathematical modeling has proven to be a powerful ally in this field, scaling results from animal models to humans, and designing optimized treatment regimens. Here we outline existing mathematical approaches for studying bone marrow toxicity, identify gaps in current understanding, and make future recommendations to advance this vital field of safety research further.
Collapse
Affiliation(s)
- Chiara Fornari
- Safety and ADME Translational Sciences, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | | | - James W T Yates
- DMPK, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - S Y Amy Cheung
- Quantitative Clinical Pharmacology, Early Clinical Development, IMED Biotech Unit, Cambridge, UK
| | - Duncan I Jodrell
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Jerome T Mettetal
- Safety and ADME Translational Sciences, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts, USA
| | - Teresa A Collins
- Safety and ADME Translational Sciences, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| |
Collapse
|
40
|
Limi S, Senecal A, Coleman R, Lopez-Jones M, Guo P, Polumbo C, Singer RH, Skoultchi AI, Cvekl A. Transcriptional burst fraction and size dynamics during lens fiber cell differentiation and detailed insights into the denucleation process. J Biol Chem 2018; 293:13176-13190. [PMID: 29959226 DOI: 10.1074/jbc.ra118.001927] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 06/11/2018] [Indexed: 01/05/2023] Open
Abstract
Genes are transcribed in irregular pulses of activity termed transcriptional bursts. Cellular differentiation requires coordinated gene expression; however, it is unknown whether the burst fraction (i.e. the number of active phases of transcription) or size/intensity (the number of RNA molecules produced within a burst) changes during cell differentiation. In the ocular lens, the positions of lens fiber cells correlate precisely with their differentiation status, and the most advanced cells degrade their nuclei. Here, we examined the transcriptional parameters of the β-actin and lens differentiation-specific α-, β-, and γ-crystallin genes by RNA fluorescent in situ hybridization (FISH) in the lenses of embryonic day (E) E12.5, E14.5, and E16.5 mouse embryos and newborns. We found that cellular differentiation dramatically alters the burst fraction in synchronized waves across the lens fiber cell compartment with less dramatic changes in burst intensity. Surprisingly, we observed nascent transcription of multiple genes in nuclei just before nuclear destruction. Nuclear condensation was accompanied by transfer of nuclear proteins, including histone and nonhistone proteins, to the cytoplasm. Although lens-specific deletion of the chromatin remodeler SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (Smarca5/Snf2h) interfered with denucleation, persisting nuclei remained transcriptionally competent and exhibited changes in both burst intensity and fraction depending on the gene examined. Our results uncover the mechanisms of nascent transcriptional control during differentiation and chromatin remodeling, confirm the burst fraction as the major factor adjusting gene expression levels, and reveal transcriptional competence of fiber cell nuclei even as they approach disintegration.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Robert H Singer
- Anatomy and Structural Biology.,Cell Biology.,Neuroscience, and
| | | | - Ales Cvekl
- From the Departments of Genetics, .,Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York 10461
| |
Collapse
|
41
|
Quantitative translational modeling to facilitate preclinical to clinical efficacy & toxicity translation in oncology. Future Sci OA 2018; 4:FSO306. [PMID: 29796306 PMCID: PMC5961452 DOI: 10.4155/fsoa-2017-0152] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
Significant scientific advances in biomedical research have expanded our knowledge of the molecular basis of carcinogenesis, mechanisms of cancer growth, and the importance of the cancer immunity cycle. However, despite scientific advances in the understanding of cancer biology, the success rate of oncology drug development remains the lowest among all therapeutic areas. In this review, some of the key translational drug development objectives in oncology will be outlined. The literature evidence of how mathematical modeling could be used to build a unifying framework to answer these questions will be summarized with recommendations on the strategies for building such a mathematical framework to facilitate the prediction of clinical efficacy and toxicity of investigational antineoplastic agents. Together, the literature evidence suggests that a rigorous and unifying preclinical to clinical translational framework based on mathematical models is extremely valuable for making go/no-go decisions in preclinical development, and for planning early clinical studies.
Collapse
|
42
|
PDGFRα+ pericryptal stromal cells are the critical source of Wnts and RSPO3 for murine intestinal stem cells in vivo. Proc Natl Acad Sci U S A 2018; 115:E3173-E3181. [PMID: 29559533 PMCID: PMC5889626 DOI: 10.1073/pnas.1713510115] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tissue stem cells in vivo reside in highly structured niches that provide signals for proliferation and differentiation. Understanding the role of the niche requires identifying the key cell types that provide these regulators. In the intestine, R-spondins and Wnts are essential regulators of the stem-cell niche. Here we identify subepithelial myofibroblasts of the PDGF receptor α lineage as the specific stromal cell type that secretes these ligands. These data demonstrate the close interaction between epithelial stem cells and the underlying regulatory stroma niche and provide insights into both normal homeostasis and tissue recovery after injury. Wnts and R-spondins (RSPOs) support intestinal homeostasis by regulating crypt cell proliferation and differentiation. Ex vivo, Wnts secreted by Paneth cells in organoids can regulate the proliferation and differentiation of Lgr5-expressing intestinal stem cells. However, in vivo, Paneth cell and indeed all epithelial Wnt production is completely dispensable, and the cellular source of Wnts and RSPOs that maintain the intestinal stem-cell niche is not known. Here we investigated both the source and the functional role of stromal Wnts and RSPO3 in regulation of intestinal homeostasis. RSPO3 is highly expressed in pericryptal myofibroblasts in the lamina propria and is several orders of magnitude more potent than RSPO1 in stimulating both Wnt/β-catenin signaling and organoid growth. Stromal Rspo3 ablation ex vivo resulted in markedly decreased organoid growth that was rescued by exogenous RSPO3 protein. Pdgf receptor alpha (PdgfRα) is known to be expressed in pericryptal myofibroblasts. We therefore evaluated if PdgfRα identified the key stromal niche cells. In vivo, Porcn excision in PdgfRα+ cells blocked intestinal crypt formation, demonstrating that Wnt production in the stroma is both necessary and sufficient to support the intestinal stem-cell niche. Mice with Rspo3 excision in the PdgfRα+ cells had decreased intestinal crypt Wnt/β-catenin signaling and Paneth cell differentiation and were hypersensitive when stressed with dextran sodium sulfate. The data support a model of the intestinal stem-cell niche regulated by both Wnts and RSPO3 supplied predominantly by stromal pericryptal myofibroblasts marked by PdgfRα.
Collapse
|
43
|
Fendrik AJ, Romanelli L, Rotondo E. Neutral dynamics and cell renewal of colonic crypts in homeostatic regime. Phys Biol 2018; 15:036003. [PMID: 29381141 DOI: 10.1088/1478-3975/aaab9f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The self renewal process in colonic crypts is the object of several studies. We present here a new compartment model with the following characteristics: (a) we distinguish different classes of cells: stem cells, six generations of transit amplifying cells and the differentiated cells; (b) in order to take into account the monoclonal character of crypts in homeostatic regimes we include symmetric divisions of the stem cells. We first consider the dynamic differential equations that describe the evolution of the mean values of the populations, but the small observed value of the total number of cells involved plus the huge dispersion of experimental data found in the literature leads us to study the stochastic discrete process. This analysis allows us to study fluctuations, the neutral drift that leads to monoclonality, and the effects of the fixation of mutant clones.
Collapse
Affiliation(s)
- A J Fendrik
- Instituto de Ciencias, Universidad Nacional de General Sarmiento-J.M.Gutierrez 1150, (1613) Los Polvorines, Buenos Aires, Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas- Buenos Aires, Argentina. Author to whom any correspondence should be addressed
| | | | | |
Collapse
|
44
|
Renardy M, Jilkine A, Shahriyari L, Chou CS. Control of cell fraction and population recovery during tissue regeneration in stem cell lineages. J Theor Biol 2018; 445:33-50. [PMID: 29470992 DOI: 10.1016/j.jtbi.2018.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 01/24/2018] [Accepted: 02/19/2018] [Indexed: 12/20/2022]
Abstract
Multicellular tissues are continually turning over, and homeostasis is maintained through regulated proliferation and differentiation of stem cells and progenitors. Following tissue injury, a dramatic increase in cell proliferation is commonly observed, resulting in rapid restoration of tissue size. This regulation is thought to occur via multiple feedback loops acting on cell self-renewal or differentiation. Models of ordinary differential equations have been widely used to study the cell lineage system. Prior modeling studies have suggested that loss of homeostasis and initiation of tumorigenesis can be contributed to the loss of control of these processes, and the rate of symmetric versus asymmetric division of the stem cells may also be altered. While most of the previous works focused on analysis of stability, existence and uniqueness of steady states of multistage cell lineage models, in this work we attempt to understand the cell lineage model from a different perspective. We compare three variants of hierarchical stem cell lineage tissue models with different combinations of negative feedbacks and use sensitivity analysis to examine the possible strategies for the cells to achieve certain performance objectives. Our results suggest that multiple negative feedback loops must be present in the stem cell lineage to keep the fractions of stem cells to differentiated cells in the total population as robust as possible to variations in cell division parameters, and to minimize the time for tissue recovery in a non-oscillatory manner.
Collapse
Affiliation(s)
- Marissa Renardy
- Department of Mathematics, Ohio State University, Columbus, OH, USA
| | - Alexandra Jilkine
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN, USA
| | - Leili Shahriyari
- Mathematical Biosciences Institute, Ohio State University, Columbus, OH, USA
| | - Ching-Shan Chou
- Department of Mathematics, Ohio State University, Columbus, OH, USA; Mathematical Biosciences Institute, Ohio State University, Columbus, OH, USA.
| |
Collapse
|
45
|
Tierney MT, Stec MJ, Rulands S, Simons BD, Sacco A. Muscle Stem Cells Exhibit Distinct Clonal Dynamics in Response to Tissue Repair and Homeostatic Aging. Cell Stem Cell 2018; 22:119-127.e3. [PMID: 29249462 PMCID: PMC5945549 DOI: 10.1016/j.stem.2017.11.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/15/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
The clonal complexity of adult stem cell pools is progressively lost during homeostatic turnover in several tissues, suggesting a decrease in the number of stem cells with distinct clonal origins. The functional impact of reduced complexity on stem cell pools, and how different tissue microenvironments may contribute to such a reduction, are poorly understood. Here, we performed clonal multicolor lineage tracing of skeletal muscle stem cells (MuSCs) to address these questions. We found that MuSC clonal complexity is maintained during aging despite heterogenous reductions in proliferative capacity, allowing aged muscle to mount a clonally diverse, albeit diminished, response to injury. In contrast, repeated bouts of tissue repair cause a progressive reduction in MuSC clonal complexity indicative of neutral drift. Consistently, biostatistical modeling suggests that MuSCs undergo symmetric expansions with stochastic fate acquisition during tissue repair. These findings establish distinct principles that underlie stem cell dynamics during homeostatic aging and muscle regeneration.
Collapse
Affiliation(s)
- Matthew T Tierney
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA; Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael J Stec
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Steffen Rulands
- Cavendish Laboratory, Department of Physics, J. J. Thomson Avenue, Cambridge CB3 0HE, UK; The Wellcome Trust/Cancer Research UK Gurdon Institute and Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Benjamin D Simons
- Cavendish Laboratory, Department of Physics, J. J. Thomson Avenue, Cambridge CB3 0HE, UK; The Wellcome Trust/Cancer Research UK Gurdon Institute and Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Alessandra Sacco
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
46
|
Kong B, Bruns P, Behler NA, Chang L, Schlitter AM, Cao J, Gewies A, Ruland J, Fritzsche S, Valkovskaya N, Jian Z, Regel I, Raulefs S, Irmler M, Beckers J, Friess H, Erkan M, Mueller NS, Roth S, Hackert T, Esposito I, Theis FJ, Kleeff J, Michalski CW. Dynamic landscape of pancreatic carcinogenesis reveals early molecular networks of malignancy. Gut 2018; 67:146-156. [PMID: 27646934 DOI: 10.1136/gutjnl-2015-310913] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The initial steps of pancreatic regeneration versus carcinogenesis are insufficiently understood. Although a combination of oncogenic Kras and inflammation has been shown to induce malignancy, molecular networks of early carcinogenesis remain poorly defined. DESIGN We compared early events during inflammation, regeneration and carcinogenesis on histological and transcriptional levels with a high temporal resolution using a well-established mouse model of pancreatitis and of inflammation-accelerated KrasG12D-driven pancreatic ductal adenocarcinoma. Quantitative expression data were analysed and extensively modelled in silico. RESULTS We defined three distinctive phases-termed inflammation, regeneration and refinement-following induction of moderate acute pancreatitis in wild-type mice. These corresponded to different waves of proliferation of mesenchymal, progenitor-like and acinar cells. Pancreas regeneration required a coordinated transition of proliferation between progenitor-like and acinar cells. In mice harbouring an oncogenic Kras mutation and challenged with pancreatitis, there was an extended inflammatory phase and a parallel, continuous proliferation of mesenchymal, progenitor-like and acinar cells. Analysis of high-resolution transcriptional data from wild-type animals revealed that organ regeneration relied on a complex interaction of a gene network that normally governs acinar cell homeostasis, exocrine specification and intercellular signalling. In mice with oncogenic Kras, a specific carcinogenic signature was found, which was preserved in full-blown mouse pancreas cancer. CONCLUSIONS These data define a transcriptional signature of early pancreatic carcinogenesis and a molecular network driving formation of preneoplastic lesions, which allows for more targeted biomarker development in order to detect cancer earlier in patients with pancreatitis.
Collapse
Affiliation(s)
- Bo Kong
- Department of Surgery, Technische Universität München (TUM), Munich, Germany.,Department of Gastroenterology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
| | - Philipp Bruns
- Department of Surgery, Technische Universität München (TUM), Munich, Germany.,Institute of Computational Biology, Helmholtz-Zentrum München GmbH, Neuherberg, Germany
| | - Nora A Behler
- Department of Surgery, Technische Universität München (TUM), Munich, Germany
| | - Ligong Chang
- Department of Surgery, Technische Universität München (TUM), Munich, Germany
| | | | - Jing Cao
- Department of Surgery, Technische Universität München (TUM), Munich, Germany
| | - Andreas Gewies
- Institute für Klinische Chemie und Pathobiochemie, TUM, Munich, Germany.,Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, Neuherberg, Germany.,German Cancer Consortium (DKTK) at the partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen Ruland
- Institute für Klinische Chemie und Pathobiochemie, TUM, Munich, Germany.,German Cancer Consortium (DKTK) at the partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Sina Fritzsche
- Department of Surgery, Technische Universität München (TUM), Munich, Germany
| | | | - Ziying Jian
- Department of Surgery, Technische Universität München (TUM), Munich, Germany
| | - Ivonne Regel
- Institute of Pathology, Heinrich-Heine University, Duesseldorf, Germany
| | - Susanne Raulefs
- Department of Surgery, Technische Universität München (TUM), Munich, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München GmbH, Neuherberg, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum München GmbH, Neuherberg, Germany.,Chair of Experimental Genetics, Technische Universität München, Freising, Germany.,Deutsches Zentrum für Diabetesforschung, Neuherberg, Germany
| | - Helmut Friess
- Department of Surgery, Technische Universität München (TUM), Munich, Germany
| | - Mert Erkan
- Department of Surgery, Koc University, Istanbul, Turkey
| | - Nikola S Mueller
- Institute of Computational Biology, Helmholtz-Zentrum München GmbH, Neuherberg, Germany
| | - Susanne Roth
- Department of Surgery, University of Heidelberg, Heidelberg, Germany
| | - Thilo Hackert
- Department of Surgery, University of Heidelberg, Heidelberg, Germany
| | - Irene Esposito
- Institute of Pathology, Heinrich-Heine University, Duesseldorf, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz-Zentrum München GmbH, Neuherberg, Germany.,Department of Mathematics, TUM, Munich, Germany
| | - Jörg Kleeff
- Department of Surgery, Technische Universität München (TUM), Munich, Germany.,NIHR Pancreas Biomedical Research Unit, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | | |
Collapse
|
47
|
Cell shape information is transduced through tension-independent mechanisms. Nat Commun 2017; 8:2145. [PMID: 29247198 PMCID: PMC5732205 DOI: 10.1038/s41467-017-02218-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/14/2017] [Indexed: 01/25/2023] Open
Abstract
The shape of a cell within tissues can represent the history of chemical and physical signals that it encounters, but can information from cell shape regulate cellular phenotype independently? Using optimal control theory to constrain reaction-diffusion schemes that are dependent on different surface-to-volume relationships, we find that information from cell shape can be resolved from mechanical signals. We used microfabricated 3-D biomimetic chips to validate predictions that shape-sensing occurs in a tension-independent manner through integrin β3 signaling pathway in human kidney podocytes and smooth muscle cells. Differential proteomics and functional ablation assays indicate that integrin β3 is critical in transduction of shape signals through ezrin–radixin–moesin (ERM) family. We used experimentally determined diffusion coefficients and experimentally validated simulations to show that shape sensing is an emergent cellular property enabled by multiple molecular characteristics of integrin β3. We conclude that 3-D cell shape information, transduced through tension-independent mechanisms, can regulate phenotype. It is not known whether the shape of a cell can regulate cellular phenotype independently. Here, the authors show that culturing kidney podocytes or smooth muscle cells on 3-D biomimetic surfaces results in phenotypic changes and that cell shape is sensed by integrin β3 in a tension-independent manner.
Collapse
|
48
|
Shankaran H, Cronin A, Barnes J, Sharma P, Tolsma J, Jasper P, Mettetal JT. Systems Pharmacology Model of Gastrointestinal Damage Predicts Species Differences and Optimizes Clinical Dosing Schedules. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2017; 7:26-33. [PMID: 28941225 PMCID: PMC5784737 DOI: 10.1002/psp4.12255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/08/2017] [Accepted: 09/18/2017] [Indexed: 12/14/2022]
Abstract
Gastrointestinal (GI) adverse events (AEs) are frequently dose limiting for oncology agents, requiring extensive clinical testing of alternative schedules to identify optimal dosing regimens. Here, we develop a translational mathematical model to predict these clinical AEs starting from preclinical GI toxicity data. The model structure incorporates known biology and includes stem cells, daughter cells, and enterocytes. Published data, including cellular numbers and division times, informed the system parameters for humans and rats. The drug‐specific parameters were informed with preclinical histopathology data from rats treated with irinotecan. The model fit the rodent irinotecan‐induced pathology changes well. The predicted time course of enterocyte loss in patients treated with weekly doses matched observed AE profiles. The model also correctly predicts a lower level of AEs for every 3 weeks (Q3W), as compared to the weekly schedule.
Collapse
Affiliation(s)
- Harish Shankaran
- Drug Safety and MetabolismIMED Biotech Unit, AstraZenecaWalthamMassachusettsUSA
| | - Anna Cronin
- Drug Safety and MetabolismIMED Biotech UnityAstraZenecaCambridgeUK
| | - Jen Barnes
- Drug Safety and MetabolismIMED Biotech UnityAstraZenecaCambridgeUK
| | - Pradeep Sharma
- Drug Safety and MetabolismIMED Biotech UnityAstraZenecaCambridgeUK
| | | | | | - Jerome T. Mettetal
- Drug Safety and MetabolismIMED Biotech Unit, AstraZenecaWalthamMassachusettsUSA
| |
Collapse
|
49
|
Stem cell self-renewal in regeneration and cancer: Insights from mathematical modeling. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.09.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
50
|
Larsen HL, Martín-Coll L, Nielsen AV, Wright CVE, Trusina A, Kim YH, Grapin-Botton A. Stochastic priming and spatial cues orchestrate heterogeneous clonal contribution to mouse pancreas organogenesis. Nat Commun 2017; 8:605. [PMID: 28928395 PMCID: PMC5605525 DOI: 10.1038/s41467-017-00258-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 06/15/2017] [Indexed: 12/16/2022] Open
Abstract
Spatiotemporal balancing of cellular proliferation and differentiation is crucial for postnatal tissue homoeostasis and organogenesis. During embryonic development, pancreatic progenitors simultaneously proliferate and differentiate into the endocrine, ductal and acinar lineages. Using in vivo clonal analysis in the founder population of the pancreas here we reveal highly heterogeneous contribution of single progenitors to organ formation. While some progenitors are bona fide multipotent and contribute progeny to all major pancreatic cell lineages, we also identify numerous unipotent endocrine and ducto-endocrine bipotent clones. Single-cell transcriptional profiling at E9.5 reveals that endocrine-committed cells are molecularly distinct, whereas multipotent and bipotent progenitors do not exhibit different expression profiles. Clone size and composition support a probabilistic model of cell fate allocation and in silico simulations predict a transient wave of acinar differentiation around E11.5, while endocrine differentiation is proportionally decreased. Increased proliferative capacity of outer progenitors is further proposed to impact clonal expansion. The pancreas arises from a small population of cells but how individual cells contribute to organ formation is unclear. Here, the authors deconstruct pancreas organogenesis into clonal units, showing that single progenitors give rise to heterogeneous multi-lineage and endocrinogenic single-lineage clones.
Collapse
Affiliation(s)
- Hjalte List Larsen
- DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200, Copenhagen N, Denmark
| | - Laura Martín-Coll
- DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200, Copenhagen N, Denmark
| | | | - Christopher V E Wright
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, 37232-0494, USA
| | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, 17 Blegdamsvej, DK-2200, Copenhagen N, Denmark
| | - Yung Hae Kim
- DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200, Copenhagen N, Denmark.
| | - Anne Grapin-Botton
- DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200, Copenhagen N, Denmark.
| |
Collapse
|