Reconstruction of Contemporary Human Stem Cell Dynamics with Oscillatory Molecular Clocks

Molecular clocks record cellular ancestry. However, currently used clocks 'tick too slowly' to measure the short-timescale dynamics of cellular renewal in adult tissues. Here we develop 'rapidly oscillating DNA methylation clocks' where ongoing (de)methylation causes the clock to 'tick-tock' back-and-forth between methylated and unmethylated states like a pendulum. We identify oscillators using standard methylation arrays and develop a mathematical modelling framework to quantitatively measure human adult stem cell dynamics from these data. Small intestinal crypts were inferred to contain slightly more stem cells than colon (6.5 ± 1.0 vs 5.8 ± 1.7 stem cells/crypt) with slower stem cell replacement in small intestine (0.79 ± 0.5 vs 1.1 ± 0.8 replacements/stem cell/year). Germline APC mutation increased the number of replacements per crypt (13.0 ± 2.4 replacements/crypt/year vs 6.9 ± 4.6 for healthy colon). In blood, we measure rapid expansion of acute leukaemia and slower growth of chronic disease. Rapidly oscillating molecular clocks are a new methodology to quantitatively measure human somatic cell dynamics.

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Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues

Nature Biotechnology ◽

10.1038/s41587-021-01109-w ◽

2022 ◽

Author(s):

Calum Gabbutt ◽

Ryan O. Schenck ◽

Daniel J. Weisenberger ◽

Christopher Kimberley ◽

Alison Berner ◽

...

Keyword(s):

Stem Cell ◽

Cell Lineage ◽

Adult Stem Cell ◽

Lineage Tracing ◽

Rapid Expansion ◽

High Temporal Resolution ◽

Molecular Clocks ◽

Cell Renewal ◽

Cell Dynamics ◽

Small Intestinal

AbstractMolecular clocks that record cell ancestry mutate too slowly to measure the short-timescale dynamics of cell renewal in adult tissues. Here, we show that fluctuating DNA methylation marks can be used as clocks in cells where ongoing methylation and demethylation cause repeated ‘flip–flops’ between methylated and unmethylated states. We identify endogenous fluctuating CpG (fCpG) sites using standard methylation arrays and develop a mathematical model to quantitatively measure human adult stem cell dynamics from these data. Small intestinal crypts were inferred to contain slightly more stem cells than the colon, with slower stem cell replacement in the small intestine. Germline APC mutation increased the number of replacements per crypt. In blood, we measured rapid expansion of acute leukemia and slower growth of chronic disease. Thus, the patterns of human somatic cell birth and death are measurable with fluctuating methylation clocks (FMCs).

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GSK3β, a Master Kinase in the Regulation of Adult Stem Cell Behavior

Cells ◽

10.3390/cells10020225 ◽

2021 ◽

Vol 10 (2) ◽

pp. 225

Author(s):

Claire Racaud-Sultan ◽

Nathalie Vergnolle

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Adult Stem Cells ◽

Glycogen Synthase ◽

Inflammatory Diseases ◽

Adult Stem Cell ◽

Leukemic Cells ◽

Cell Phenotype ◽

Epithelial Regeneration ◽

Cell Functions

In adult stem cells, Glycogen Synthase Kinase 3β (GSK3β) is at the crossroad of signaling pathways controlling survival, proliferation, adhesion and differentiation. The microenvironment plays a key role in the regulation of these cell functions and we have demonstrated that the GSK3β activity is strongly dependent on the engagement of integrins and protease-activated receptors (PARs). Downstream of the integrin α5β1 or PAR2 activation, a molecular complex is organized around the scaffolding proteins RACK1 and β-arrestin-2 respectively, containing the phosphatase PP2A responsible for GSK3β activation. As a consequence, a quiescent stem cell phenotype is established with high capacities to face apoptotic and metabolic stresses. A protective role of GSK3β has been found for hematopoietic and intestinal stem cells. Latters survived to de-adhesion through PAR2 activation, whereas formers were protected from cytotoxicity through α5β1 engagement. However, a prolonged activation of GSK3β promoted a defect in epithelial regeneration and a resistance to chemotherapy of leukemic cells, paving the way to chronic inflammatory diseases and to cancer resurgence, respectively. In both cases, a sexual dimorphism was measured in GSK3β-dependent cellular functions. GSK3β activity is a key marker for inflammatory and cancer diseases allowing adjusted therapy to sex, age and metabolic status of patients.

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Article Commentary: Stem Cell Research in Cell Transplantation: An Analysis of Geopolitical Influence by Publications

Cell Transplantation ◽

10.3727/000000007783465190 ◽

2007 ◽

Vol 16 (8) ◽

pp. 867-873 ◽

Cited By ~ 5

Author(s):

David J. Eve ◽

Paul R. Sanberg

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Cell Transplantation ◽

Adult Stem Cells ◽

Adult Stem Cell ◽

Therapeutic Area ◽

Fetal Stem Cells ◽

Major Player ◽

The Us ◽

Restricted Use

One of the fastest growing fields in researching treatments for neurodegenerative and other disorders is the use of stem cells. These cells are naturally occurring and can be obtained from three different stages of an organism's life: embryonic, fetal, and adult. In the US, political doctrine has restricted use of federal funds for stem cells, enhancing research towards an adult source. In order to determine how this legislation may be represented by the stem cell field, a retrospective analysis of stem cell articles published in the journal Cell Transplantation over a 2-year period was performed. Cell Transplantation is considered a translational journal from preclinical to clinical, so it was of interest to determine the publication outcome of stem cell articles 6 years after the US regulations. The distribution of the source of stem cells was found to be biased towards the adult stage, but relatively similar over the embryonic and fetal stages. The fetal stem cell reports were primarily neural in origin, whereas the adult stem cell ones were predominantly mesenchymal and used mainly in neural studies. The majority of stem cell studies published in Cell Transplantation were found to fall under the umbrella of neuroscience research. American scientists published the most articles using stem cells with a bias towards adult stem cells, supporting the effect of the legislation, whereas Europe was the leading continent with a bias towards embryonic and fetal stem cells, where research is “controlled” but not restricted. Japan was also a major player in the use of stem cells. Allogeneic transplants (where donor and recipient are the same species) were the most common transplants recorded, although the transplantation of human-derived stem cells into rodents was the most common specific transplantation performed. This demonstrates that the use of stem cells is an increasingly important field (with a doubling of papers between 2005 and 2006), which is likely to develop into a major therapeutic area over the next few decades and that funding restrictions can affect the type of research being performed.

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Comparative characterization and osteogenic / adipogenic differentiation of mesenchymal stem cells derived from male rat hair follicles and bone marrow

Cell Regeneration ◽

10.1186/s13619-020-00051-7 ◽

2020 ◽

Vol 9 (1) ◽

Author(s):

Abdel Kader A. Zaki ◽

Tariq I. Almundarij ◽

Faten A. M. Abo-Aziza

Keyword(s):

Stem Cells ◽

Bone Marrow ◽

Mesenchymal Stem Cells ◽

Stem Cell ◽

Adipogenic Differentiation ◽

Adult Stem Cell ◽

Cell Counting ◽

Population Doubling ◽

Male Rat ◽

Cell Source

AbstractClinical applications of cell therapy and tissue regeneration under different conditions need a multiplicity of adult stem cell sources. Up to date, little is available on the comparative isolation, characterization, proliferation, rapid amplification, and osteogenic/adipogenic differentiation of rat mesenchymal stem cells (MSCs) isolated from living bulge cells of the hair follicle (HF) and bone marrow (BM) from the same animal. This work hopes to use HF-MSCs as an additional adult stem cell source for research and application. After reaching 80% confluence, the cell counting, viability %, and yields of HF-MSCs and BM-MSCs were nearly similar. The viability % was 91.41 ± 2.98 and 93.11 ± 3.06 while the cells yield of initial seeding was 33.15 ± 2.76 and 34.22 ± 3.99 and of second passage was 28.76 ± 1.01 and 29.56 ± 3.11 for HF-MSCs and BM-MSCs respectively. Clusters of differentiation (CDs) analysis revealed that HF-MSCs were positively expressed CD34, CD73 and CD200 and negatively expressed CD45. BM-MSCs were positively expressed CD73 and CD200 and negatively expressed of CD34 and CD45. The proliferation of HF-MSCs and BM-MSCs was determined by means of incorporation of Brd-U, population doubling time (PDT) assays and the quantity of formazan release. The percentage of Brd-U positive cells and PDT were relatively similar in both types of cells. The proliferation, as expressed by the quantity of formazan assay in confluent cells, revealed that the quantity of release by BM-MSCs was slightly higher than HF-MSCs. Adipogenic differentiated BM-MSCs showed moderate accumulation of oil red-O stained lipid droplets when compared to that of HF-MSCs which exhibited high stain. The total lipid concentration was significantly higher in adipogenic differentiated HF-MSCs than BM-MSCs (P < 0.05). It was found that activity of bone alkaline phosphatase and calcium concentration were significantly higher (P < 0.01 and P < 0.05 respectively) in osteogenic differentiated BM-MSCs than that of HF-MSCs. The present findings demonstrate that the HF-MSCs are very similar in most tested characteristics to BM-MSCs with the exception of differentiation. Additionally; no issues have been reported during the collection of HF-MSCs. Therefore, the HF may represent a suitable and accessible source for adult stem cells and can be considered an ideal cell source for adipogenesis research.

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Transforming growth factor-?3 protects murine small intestinal crypt stem cells and animal survival after irradiation, possibly by reducing stem-cell cycling

International Journal of Cancer ◽

10.1002/(sici)1097-0215(20000401)86:1<53::aid-ijc8>3.0.co;2-z ◽

2000 ◽

Vol 86 (1) ◽

pp. 53-59 ◽

Cited By ~ 60

Author(s):

Dawn Booth ◽

John D. Haley ◽

Arthur M. Bruskin ◽

Christopher S. Potten

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Growth Factor ◽

Transforming Growth Factor ◽

Intestinal Crypt ◽

Animal Survival ◽

Small Intestinal ◽

Cell Cycling

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Loss of foxo rescues stem cell aging in Drosophila germ line

eLife ◽

10.7554/elife.27842 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 8

Author(s):

Filippo Artoni ◽

Rebecca E Kreipke ◽

Ondina Palmeira ◽

Connor Dixon ◽

Zachary Goldberg ◽

...

Keyword(s):

Cell Cycle ◽

Stem Cells ◽

Stem Cell ◽

Ionizing Radiation ◽

Cell Injury ◽

Germ Line ◽

Adult Stem Cell ◽

Cell Aging ◽

Germline Stem Cells ◽

Cell Cycle Reentry

Aging stem cells lose the capacity to properly respond to injury and regenerate their residing tissues. Here, we utilized the ability of Drosophila melanogaster germline stem cells (GSCs) to survive exposure to low doses of ionizing radiation (IR) as a model of adult stem cell injury and identified a regeneration defect in aging GSCs: while aging GSCs survive exposure to IR, they fail to reenter the cell cycle and regenerate the germline in a timely manner. Mechanistically, we identify foxo and mTOR homologue, Tor as important regulators of GSC quiescence following exposure to ionizing radiation. foxo is required for entry in quiescence, while Tor is essential for cell cycle reentry. Importantly, we further show that the lack of regeneration in aging germ line stem cells after IR can be rescued by loss of foxo.

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Chondrogenic priming of human fetal synovium-derived stem cells in an adult stem cell matrix microenvironment

Genes & Diseases ◽

10.1016/j.gendis.2015.06.004 ◽

2015 ◽

Vol 2 (4) ◽

pp. 337-346 ◽

Cited By ~ 1

Author(s):

Jingting Li ◽

Fan He ◽

Ming Pei

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Adult Stem Cell ◽

Cell Matrix

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Troy+ brain stem cells cycle through quiescence and regulate their number by sensing niche occupancy

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1715911114 ◽

2018 ◽

Vol 115 (4) ◽

pp. E610-E619 ◽

Cited By ~ 56

Author(s):

Onur Basak ◽

Teresa G. Krieger ◽

Mauro J. Muraro ◽

Kay Wiebrands ◽

Daniel E. Stange ◽

...

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Cell Number ◽

Lineage Tracing ◽

Rapid Expansion ◽

Molecular Signature ◽

Genetic Lineage ◽

Proliferating Cells ◽

Self Renewal ◽

Genetic Lineage Tracing

The adult mouse subependymal zone provides a niche for mammalian neural stem cells (NSCs). However, the molecular signature, self-renewal potential, and fate behavior of NSCs remain poorly defined. Here we propose a model in which the fate of active NSCs is coupled to the total number of neighboring NSCs in a shared niche. Using knock-in reporter alleles and single-cell RNA sequencing, we show that the Wnt target Tnfrsf19/Troy identifies both active and quiescent NSCs. Quantitative analysis of genetic lineage tracing of individual NSCs under homeostasis or in response to injury reveals rapid expansion of stem-cell number before some return to quiescence. This behavior is best explained by stochastic fate decisions, where stem-cell number within a shared niche fluctuates over time. Fate mapping proliferating cells using a Ki67iresCreER allele confirms that active NSCs reversibly return to quiescence, achieving long-term self-renewal. Our findings suggest a niche-based mechanism for the regulation of NSC fate and number.

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Strategic Tools in Regenerative and Translational Dentistry

International Journal of Molecular Sciences ◽

10.3390/ijms20081879 ◽

2019 ◽

Vol 20 (8) ◽

pp. 1879 ◽

Cited By ~ 5

Author(s):

Marco Tatullo ◽

Bruna Codispoti ◽

Francesco Paduano ◽

Manuel Nuzzolese ◽

Irina Makeeva

Keyword(s):

Stem Cells ◽

Stem Cell ◽

State Of The Art ◽

Adult Stem Cell ◽

Point Of View ◽

Local Inflammation ◽

Differentiation Potential ◽

Clear Point ◽

Regenerative Ability ◽

Stem Cell Populations

Human oral-derived stem cells can be easily obtained from several oral tissues, such as dental pulp, periodontal ligament, from gingiva, or periapical cysts. Due to their differentiation potential, oral-derived mesenchymal stem cells are promising for tissue engineering and regenerative medicine. The regenerative ability showed by some oral tissues strongly depends on their sleeping adult stem cell populations that are able to repair small defects and to manage local inflammation. To date, researchers are working on effective and efficient methods to ensure safe and predictable protocols to translate stem cell research into human models. In the last decades, the challenge has been to finally use oral-derived stem cells together with biomaterials or scaffold-free techniques, to obtain strategic tools for regenerative and translational dentistry. This paper aims to give a clear point of view on state of the art developments, with some exciting insights into future strategies.

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