Methylation patterns and mathematical models reveal dynamics of stem cell turnover in the human colon

A Systematic Review of Fibonacci Sequence in the Human Abdominal Wall: Facts and Reality

The Fibonacci sequence is undoubtedly found in nature such as in the spiral of galaxies and flower petals. Fibonacci numbers are a sequence in which each number is the sum of the two preceding ones. The ratio of two consecutive Fibonacci numbers, also called the golden proportion, approximately equals 1.618. We analyzed the existence of Fibonacci numbers and golden ratios in the field of hernia and abdominal wall reconstruction. We found substantial evidence of the use of the golden ratio in siting of the umbilicus. The Fibonacci numbers also showed up frequently in the anatomy of the abdominal wall. However, this was not as appropriate as the other instances in the human body or in nature.

Cellular and epigenetic drivers of stem cell ageing

Adult tissue stem cells have a pivotal role in tissue maintenance and regeneration throughout the lifespan of multicellular organisms. Loss of tissue homeostasis during post-reproductive lifespan is caused, at least in part, by a decline in stem cell function and is associated with an increased incidence of diseases. Hallmarks of ageing include the accumulation of molecular damage, failure of quality control systems, metabolic changes and alterations in epigenome stability. In this Review, we discuss recent evidence in support of a novel concept whereby cell-intrinsic damage that accumulates during ageing and cell-extrinsic changes in ageing stem cell niches and the blood result in modifications of the stem cell epigenome. These cumulative epigenetic alterations in stem cells might be the cause of the deregulation of developmental pathways seen during ageing. In turn, they could confer a selective advantage to mutant and epigenetically drifted stem cells with altered self-renewal and functions, which contribute to the development of ageing-associated organ dysfunction and disease.

Computational modelling folate metabolism and DNA methylation: implications for understanding health and ageing

Dietary folates have a key role to play in health, as deficiencies in the intake of these B vitamins have been implicated in a wide variety of clinical conditions. The reason for this is folates function as single carbon donors in the synthesis of methionine and nucleotides. Moreover, folates have a vital role to play in the epigenetics of mammalian cells by supplying methyl groups for DNA methylation reactions. Intriguingly, a growing body of experimental evidence suggests that DNA methylation status could be a central modulator of the ageing process. This has important health implications because the methylation status of the human genome could be used to infer age-related disease risk. Thus, it is imperative we further our understanding of the processes which underpin DNA methylation and how these intersect with folate metabolism and ageing. The biochemical and molecular mechanisms, which underpin these processes, are complex. However, computational modelling offers an ideal framework for handling this complexity. A number of computational models have been assembled over the years, but to date, no model has represented the full scope of the interaction between the folate cycle and the reactions, which governs the DNA methylation cycle. In this review, we will discuss several of the models, which have been developed to represent these systems. In addition, we will present a rationale for developing a combined model of folate metabolism and the DNA methylation cycle.

Neutral dynamics and cell renewal of colonic crypts in homeostatic regime

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.

Multi-scale modeling of APC and [Formula: see text]-catenin regulation in the human colonic crypt

Stem cell renewal and differentiation in the human colonic crypt are linked to the [Formula: see text]-catenin pathway. The spatial balance of Wnt factors in proliferative cells within the crypt maintain an appropriate level of cellular reproduction needed for normal crypt homeostasis. Mutational events at the gene level are responsible for deregulating the balance of Wnt factors along the crypt, causing an overpopulation of proliferative cells, a loss of structure of the crypt domain, and the initiation of colorectal carcinomas. We formulate a PDE model describing cell movement and reproduction in a static crypt domain. We consider a single cell population whose proliferative capabilities are determined by stemness, a quantity defined by intracellular levels of adenomatous polyposis coli (APC) scaffold protein and [Formula: see text]-catenin. We fit APC regulation parameters to biological data that describe normal protein gradients in the crypt. We also fit cell movement and protein flux parameters to normal crypt characteristics such as renewal time, total cell count, and proportion of proliferating cells. The model is used to investigate abnormal crypt dynamics when subjected to a diminished APC gradient, a scenario synonymous to mutations in the APC gene. We find that a 25% decrease in APC synthesis leads to a fraction of 0.88 proliferative, which is reflective of normal-appearing FAP crypts. A 50% drop in APC activity yields a fully proliferative crypt showing a doubling of the level of stemness, which characterizes the initial stages of colorectal cancer development. A sensitivity analysis of APC regulation parameters shows the perturbation of factors that is required to restore crypt dynamics to normal in the case of APC mutations.

Longitudinal analysis of colon crypt stem cell dynamics in sulindac treated Familial Adenomatous Polyposis patients

The non-steroidal anti-inflammatory drug sulindac decreases size and number of adenomas after 4-6 months of treatment for familial adenomatous polyposis (FAP) patients. However, the underlying mechanism remains unknown. As stem cells are thought to be the tumor precursor cells, visualizing their behavior is crucial for monitoring tumor progression. Increased tag diversity in inactive genes is indicative of a protracted clonal evolution and consequently, increased risk for tumor formation. Therefore, the effect of sulindac on stem cell dynamics was studied. Normal appearing single crypts were laser microdissected in placebo- and sulindac- treated FAP patient tissue after which the methylation patterns were visualized by Next Generation Sequencing. A significant difference in tag diversity over time was found in the sulindac group compared to the placebo group (*p = 0.018), indicative of a shortened clonal evolution treated sulindac. The rate of change in tag diversity over time was correlated with polyp number change over time. No significant difference over time was observed in the percent methylation when comparing placebo vs sulindac. In conclusion, daily sulindac administration in FAP patients significantly altered colorectal stem cell dynamics, which might explain the chemopreventive action of this drug indicating that tag diversity may be used as a predictive biomarker.

Stem cell dynamics and pretumor progression in the intestinal tract

Colorectal carcinogenesis is a process that follows a stepwise cascade that goes from the normal to an invisible pretumor stage ultimately leading to grossly visible tumor progression. During pretumor progression, an increasing accumulation of genetic alterations occurs, by definition without visible manifestations. It is generally thought that stem cells in the crypt base are responsible for this initiation of colorectal cancer progression because they are the origin of the differentiated epithelial cells that occupy the crypt. Furthermore, they are characterized by a long life span that enables them to acquire these cumulative mutations. Recent studies visualized the dynamics of stem cells both in vitro and in vivo. Translating this work into clinical applications will contribute to the evaluation of patients' predisposition for colorectal carcinogenesis and may help in the design of preventive measures for high-risk groups. In this review, we outline the progress made in the research into tracing stem cell dynamics. Further, we highlight the importance and potential clinical value of tracing stem cell dynamics in pretumor progression.

An APC:WNT Counter-Current-Like Mechanism Regulates Cell Division Along the Human Colonic Crypt Axis: A Mechanism That Explains How APC Mutations Induce Proliferative Abnormalities That Drive Colon Cancer Development

APC normally down-regulates WNT signaling in human colon, and APC mutations cause proliferative abnormalities in premalignant crypts leading to colon cancer, but the mechanisms are unclear at the level of spatial and functional organization of the crypt. Accordingly, we postulated a counter-current-like mechanism based on gradients of factors (APC;WNT) that regulate colonocyte proliferation along the crypt axis. During crypt renewal, stem cells (SCs) at the crypt bottom generate non-SC daughter cells that proliferate and differentiate while migrating upwards. The APC concentration is low at the crypt bottom and high at the top (where differentiated cells reside). WNT signaling, in contrast, is high at the bottom (where SCs reside) and low at the top. Given that WNT and APC gradients are counter to one another, we hypothesized that a counter-current-like mechanism exists. Since both APC and WNT signaling components (e.g., survivin) are required for mitosis, this mechanism establishes a zone in the lower crypt where conditions are optimal for maximal cell division and mitosis orientation (symmetric versus asymmetric). APC haploinsufficiency diminishes the APC gradient, shifts the proliferative zone upwards, and increases symmetric division, which causes SC overpopulation. In homozygote mutant crypts, these changes are exacerbated. Thus, APC-mutation-induced changes in the counter-current-like mechanism cause expansion of proliferative populations (SCs, rapidly proliferating cells) during tumorigenesis. We propose this mechanism also drives crypt fission, functions in the crypt cycle, and underlies adenoma development. Novel chemoprevention approaches designed to normalize the two gradients and readjust the proliferative zone downwards, might thwart progression of these premalignant changes.

Mathematical modeling of monoclonal conversion in the colonic crypt

A novel spatial multiscale model of a colonic crypt is described, which couples the cell cycle (including cell division) with the mechanics of cell movement. The model is used to investigate the process of monoclonal conversion under two hypotheses concerning stem cell behavior. Under the first hypothesis, 'stem-ness' is an intrinsic cell property, and the stem cell population is maintained through asymmetric division. Under the second hypothesis, the proliferative behavior of each cell is governed by its microenvironment through a biochemical signalling cue, and all cell division is symmetric. Under each hypothesis, the model is used to run virtual experiments, in which a harmless labeling mutation is bestowed upon a single cell in the crypt and the mutant clonal population is tracked over time to check if and when the crypt becomes monoclonal. It is shown that under the first hypothesis, a stable structured cell population is not possible without some form of population-dependent feedback; in contrast, under the second hypothesis, a stable crypt architecture arises naturally. Through comparison with an existing spatial crypt model and a non-spatial stochastic population model, it is shown that the spatial structure of the crypt has a significant effect on the time scale over which a crypt becomes monoclonal.

Diversity counts. Visualizing pretumor progression in the gastrointestinal tract

Tumor progression is critically dependent on the selection of genetic alterations. This clonal evolution can be traced to the stage preceding visible tumor formation called pretumor progression, in which genetic change occurs without visible change. Recently, the identification of intestinal stem cell markers in animal models has made visualization of stem cells possible in vivo. Translating this work to the clinical setting by visualizing stem cells in patient material may allow us to understand differences in patients' vulnerability to cancer development and target preventive measures to high-risk groups. In this review article, we examine some of the analytic methods currently used in research settings tracing stem cell dynamics.

Adult stem cells in the endometrium

Rare cells with adult stem cell activity were recently discovered in human endometrium. Endometrial stem/progenitor cell candidates include epithelial, mesenchymal and endothelial cells, and all may contribute to the rapid endometrial regeneration following menstruation, rather than a single candidate. Endometrial mesenchymal stem-like cells (eMSC) are prospectively isolated as CD146(+)PDGF-Rβ(+) cells and are found in both basalis and functionalis as perivascular cells. Epithelial progenitor cells are detected in colony forming unit assays but their identity awaits elucidation. They are postulated to reside in the basalis in gland bases. Endometrial stem/progenitor cells may be derived from endogenous stem cells, but emerging evidence suggests a bone marrow contribution. Endometrial endothelial progenitor cells are detected as side population cells, which express several endothelial cell markers and differentiate into endometrial glandular epithelial, stromal and endothelial cells. Investigating endometrial stem cell biology is crucial to understanding normal endometrial physiology and to determine their roles in endometrial proliferative diseases. The nature of endometriosis suggests that initiation of ectopic endometrial lesions involves endometrial stem/progenitor cells, a notion compatible with Sampson's retrograde menstruation theory and supported by the demonstration of eMSC in menstrual blood. Evidence of cancer stem cells (CSC) in endometrial cancer indicates that new avenues for developing therapeutic options targeting CSC may become available. We provide an overview of the accumulating evidence for endometrial stem/progenitor cells and their possible roles in endometrial proliferative disorders, and discuss the unresolved issues.

Epigenetics, stem cells and epithelial cell fate

Establishment and maintenance of epigenetic profiles are essential steps of development during which stem cells, despite identical genetic information, will acquire different and selective gene expression patterns, specific for their fate. This highly complex programming process involves mechanisms that are not yet completely understood although it has been established over the past few years that chromatin modifier enzymes (i.e. DNA and histone methyltransferases, histone deacetylases, histone demethylases, histone acetyltransferases) play essential roles in the establishment of transcriptional programs accompanying cell differentiation. Investigators in this field have been studying a wide variety of cell types including neural, muscular, mesenchymal and blood cells. This review will focus on epithelial cells of the digestive tract, intestinal stem cell niches being a model of choice to understand how epigenetic changes can drive nuclear programming and specific cell differentiation. Moreover, deregulation of epigenetic programming is frequently observed in human tumours and therefore, decoding these molecular mechanisms is essential to better understand both developmental and cancerous processes.

Colonic stem cell data are consistent with the immortal model of stem cell division under non-random strand segregation

OBJECTIVES

Colonic stem cells are thought to reside towards the base of crypts of the colon, but their numbers and proliferation mechanisms are not well characterized. A defining property of stem cells is that they are able to divide asymmetrically, but it is not known whether they always divide asymmetrically (immortal model) or whether there are occasional symmetrical divisions (stochastic model). By measuring diversity of methylation patterns in colon crypt samples, a recent study found evidence in favour of the stochastic model, assuming random segregation of stem cell DNA strands during cell division. Here, the effect of preferential segregation of the template strand is considered to be consistent with the 'immortal strand hypothesis', and explore the effect on conclusions of previously published results.

MATERIALS AND METHODS

For a sample of crypts, it is shown how, under the immortal model, to calculate mean and variance of the number of unique methylation patterns allowing for non-random strand segregation and compare them with those observed.

RESULTS

The calculated mean and variance are consistent with an immortal model that incorporates non-random strand segregation for a range of stem cell numbers and levels of preferential strand segregation.

CONCLUSIONS

Allowing for preferential strand segregation considerably alters previously published conclusions relating to stem cell numbers and turnover mechanisms. Evidence in favour of the stochastic model may not be as strong as previously thought.

Asymmetric division of activated latently infected cells may explain the decay kinetics of the HIV-1 latent reservoir and intermittent viral blips

Most HIV-infected patients when treated with combination antiretroviral therapy achieve viral loads that are below the current limit of detection of standard assays after a few months. Despite this, virus eradication from the host has not been achieved. Latent, replication-competent HIV-1 can generally be identified in resting memory CD4(+) T cells in patients with "undetectable" viral loads. Turnover of these cells is extremely slow but virus can be released from the latent reservoir quickly upon cessation of therapy. In addition, a number of patients experience transient episodes of viremia, or HIV-1 blips, even with suppression of the viral load to below the limit of detection for many years. The mechanisms underlying the slow decay of the latent reservoir and the occurrence of intermittent viral blips have not been fully elucidated. In this study, we address these two issues by developing a mathematical model that explores a hypothesis about latently infected cell activation. We propose that asymmetric division of latently infected cells upon sporadic antigen encounter may both replenish the latent reservoir and generate intermittent viral blips. Interestingly, we show that occasional replenishment of the latent reservoir induced by reactivation of latently infected cells may reconcile the differences between the divergent estimates of the half-life of the latent reservoir in the literature.

Human colon cancer stem cells: a new paradigm in gastrointestinal oncology

For the past half century, oncologists have had systemic drugs available, agents that are able to induce tumor responses in patients with colorectal cancer. However, in cases of advanced colorectal cancer, these regimens are almost never curative. The recently introduced concept that cancer stem cells (SCs) drive tumor growth suggests a reason for these therapeutic failures--current chemotherapeutics target rapidly dividing cells but cancer SCs divide only slowly, and, they are relatively resistant to cytotoxic systemic therapies. It also suggests a solution--development of therapeutics that target cancer SCs. However, there is a paucity of information about the mechanisms by which SC populations are maintained and about the mechanisms by which tumor SCs are involved in colon cancer development. In this article, we discuss these mechanisms and recent developments in the identification and isolation of colon cancer SCs using new SC markers. We then discuss the role of SCs in homeostasis of normal colonic epithelium, and mechanisms by which dysregulation of crypt mechanisms can lead to initiation and progression of colon cancer. Our hypothesis, which has received recent experimental support, is that the mechanism that links abnormalities at the gene level (eg, APC mutations) and abnormalities at the tissue level (eg, proliferative shift, dysplasia, carcinoma) from cancer initiation to metastasis is SC overpopulation. Finally, we discuss the concept that symmetric cancer SC division is an essential mechanism that drives tumor growth, and that development of a new generation of therapeutics that target colon cancer SCs by inhibiting symmetric SC division holds promise for truly curative approaches for patients with advanced colorectal cancers.

How dysregulated colonic crypt dynamics cause stem cell overpopulation and initiate colon cancer

Based on investigation of the earliest colonic tissue alteration in familial adenomatous polyposis (FAP) patients, we present the hypothesis that initiation of colorectal cancer by adenomatous polyposis coli (APC) mutation is mediated by dysregulation of two cellular mechanisms. One involves differentiation, which normally decreases the proportion (proliferative fraction) of colonic crypt cells that can proliferate; the other is a cell cycle mechanism that simultaneously increases the probability that proliferative cells are in S phase. In normal crypts, stem cells (SC) at the crypt bottom generate rapidly proliferating cells, which undergo differentiation while migrating up the crypt. Our modeling of normal crypts suggests that these transitions are mediated by mechanisms that regulate proliferative fraction and S-phase probability. In FAP crypts, the population of rapidly proliferating cells is shifted upwards, as indicated by the labeling index (LI; i.e., crypt distribution of cells in S phase). Our analysis of FAP indicates that these transitions are delayed because the proliferative fraction and S-phase probability change more slowly as a function of crypt level. This leads to expansion of the proliferative cell population, including a subpopulation that has a low frequency of S-phase cells. We previously reported that crypt SC overpopulation explains the LI shift. Here, we determine that SCs (or cells having high stemness) are proliferative cells with a low probability of being in S phase. Thus, dysregulation of mechanisms that control proliferative fraction and S-phase probability explains how APC mutations induce SC overpopulation at the crypt bottom, shift the rapidly proliferating cell population upwards, and initiate colon tumorigenesis.

Stem cells as common ancestors in a colorectal cancer ancestral tree

PURPOSE OF REVIEW

Cancer is thought to be an evolutionary process. Modern studies of evolution increasingly rely on genome comparisons, and similar molecular phylogeny approaches could be translated to somatic cell genomes to reconstruct colorectal cancer progression. The purpose of this review is to outline how human somatic cell ancestral trees can organize many old and new observations.

RECENT FINDINGS

A somatic cell tree starts from the zygote and ends with present day normal or neoplastic cells. In between are ancestors and dead ends, which functionally correspond to stem and nonstem cells. Cancer genome projects illustrate that mutations are relatively infrequent, and consistent with normal mutation rates, particularly if mutations begin to accumulate from birth. Therefore, some mutations eventually found in cancers may first occur in normal appearing crypts, which are maintained by niches that allow for stem cell clonal evolution and selection. Although mutations occur too infrequently to function as somatic cell molecular clocks, potentially more labile epigenetic changes in CpG methylation may also record somatic cell ancestry.

SUMMARY

Somatic cell evolution can occur throughout life, and potentially at least some of this unseen past may be reconstructed by 'reading' the lifetime changes that accumulate within our genomes.

Stem cells and the Planarian Schmidtea mediterranea

In recent years, stem cells have been heralded as potential therapeutic agents to address a large number of degenerative diseases. Yet, in order to rationally utilize these cells as effective therapeutic agents, and/or improve treatment of stem-cell-associated malignancies such as leukemias and carcinomas, a better understanding of the basic biological properties of stem cells needs to be acquired. A major limitation in the study of stem cells lies in the difficulty of accessing and studying these cells in vivo. This barrier is further compounded by the limitations of in vitro culture systems, which are unable to emulate the microenvironments in which stem cells reside and which are known to provide critical regulatory signals for their proliferation and differentiation. Given the complexity of vertebrate embryonic and adult stem cell populations and their relative inaccessibility to in vivo molecular analyses, the study of stem cells should benefit from analyzing their counterparts in simpler model organisms. In the past, the use of Drosophila or C. elegans has provided invaluable contributions to our understanding of genes and pathways involved in a variety of human diseases. However, stem cells in these organisms are mostly restricted to the gonads, and more importantly neither Drosophila, nor C. elegans are capable of regenerating body parts lost to injury. Therefore, a simple animal with experimentally accessible stem cells playing a role in tissue maintenance and/or regeneration should be very useful in identifying and functionally testing the mechanisms regulating stem cell activities. The planarian Schmidtea mediterranea is poised to fill this experimental gap. S. mediterranea displays robust regenerative properties driven by a stem cell population capable of producing the approximately 40 different cell types found in this organism, including the germ cells. Given that all known metazoans depend on stem cells for their survival, it is extremely likely that the molecular events regulating stem cell biology would have been conserved throughout evolution, and that the knowledge derived from studying planarian stem cells could be vertically integrated to the study of vertebrate stem cells. Current efforts, therefore, are aimed at further characterizing the population of planarian stem cells in order to define its suitability as a model system in which to mechanistically dissect the basic biological attributes of metazoans stem cells.

Mathematical modeling of cell population dynamics in the colonic crypt and in colorectal cancer

Colorectal cancer is initiated in colonic crypts. A succession of genetic mutations or epigenetic changes can lead to homeostasis in the crypt being overcome, and subsequent unbounded growth. We consider the dynamics of a single colorectal crypt by using a compartmental approach [Tomlinson IPM, Bodmer WF (1995) Proc Natl Acad Sci USA 92:], which accounts for populations of stem cells, differentiated cells, and transit cells. That original model made the simplifying assumptions that each cell population divides synchronously, but we relax these assumptions by adopting an age-structured approach that models asynchronous cell division, and by using a continuum model. We discuss two mechanisms that could regulate the growth of cell numbers and maintain the equilibrium that is normally observed in the crypt. The first will always maintain an equilibrium for all parameter values, whereas the second can allow unbounded proliferation if the net per capita growth rates are large enough. Results show that an increase in cell renewal, which is equivalent to a failure of programmed cell death or of differentiation, can lead to the growth of cancers. The second model can be used to explain the long lag phases in tumor growth, during which new, higher equilibria are reached, before unlimited growth in cell numbers ensues.

Uterine stem cells: what is the evidence?

The mucosal lining (endometrium) of the human uterus undergoes cyclical processes of regeneration, differentiation and shedding as part of the menstrual cycle. Endometrial regeneration also follows parturition, almost complete resection and in post-menopausal women taking estrogen replacement therapy. In non-menstruating species, there are cycles of endometrial growth and apoptosis rather than physical shedding. The concept that endometrial stem/progenitor cells are responsible for the remarkable regenerative capacity of endometrium was proposed many years ago. However, attempts to isolate, characterize and locate endometrial stem cells have only been undertaken in the last few years as experimental approaches to identify adult stem/progenitor cells in other tissues have been developed. Adult stem cells are defined by their functional properties rather than by marker expression. Evidence for the existence of adult stem/progenitor cells in human and mouse endometrium is now emerging because functional stem cell assays are being applied to uterine cells and tissues. These fundamental studies on endometrial stem/progenitor cells will provide new insights into the pathophysiology of various gynaecological disorders associated with abnormal endometrial proliferation, including endometrial cancer, endometrial hyperplasia, endometriosis and adenomyosis.

Crypt dynamics and colorectal cancer: advances in mathematical modelling

Mathematical modelling forms a key component of systems biology, offering insights that complement and stimulate experimental studies. In this review, we illustrate the role of theoretical models in elucidating the mechanisms involved in normal intestinal crypt dynamics and colorectal cancer. We discuss a range of modelling approaches, including models that describe cell proliferation, migration, differentiation, crypt fission, genetic instability, APC inactivation and tumour heterogeneity. We focus on the model assumptions, limitations and applications, rather than on the technical details. We also present a new stochastic model for stem-cell dynamics, which predicts that, on average, APC inactivation occurs more quickly in the stem-cell pool in the absence of symmetric cell division. This suggests that natural niche succession may protect stem cells against malignant transformation in the gut. Finally, we explain how we aim to gain further understanding of the crypt system and of colorectal carcinogenesis with the aid of multiscale models that cover all levels of organization from the molecular to the whole organ.

Evolution of cancer stem cells

Cancer as a disease driven by cancer stem cells is a concept that has emerged over the last few years. However, several issues relating to this phenomenon as yet remain unaddressed. A fundamental question is one relating to the identification of events leading to transformation of a normal tissue stem cell to a cancer stem cell. Complete knowledge of this evolutionary process may be crucial for the development of novel effective therapies that influence patient prognosis. The scope of this review is to discuss reports that have begun to elucidate stem cell transformation either as an isolated event or as a progression as an attempt towards understanding some of the critical events involved in the process.

Human hair genealogies and stem cell latency

BACKGROUND

Stem cells divide to reproduce themselves and produce differentiated progeny. A fundamental problem in human biology has been the inability to measure how often stem cells divide. Although it is impossible to observe every division directly, one method for counting divisions is to count replication errors; the greater the number of divisions, the greater the numbers of errors. Stem cells with more divisions should produce progeny with more replication errors.

METHODS

To test this approach, epigenetic errors (methylation) in CpG-rich molecular clocks were measured from human hairs. Hairs exhibit growth and replacement cycles and "new" hairs physically reappear even on "old" heads. Errors may accumulate in long-lived stem cells, or in their differentiated progeny that are eventually shed.

RESULTS

Average hair errors increased until two years of age, and then were constant despite decades of replacement, consistent with new hairs arising from infrequently dividing bulge stem cells. Errors were significantly more frequent in longer hairs, consistent with long-lived but eventually shed mitotic follicle cells.

CONCLUSION

Constant average hair methylation regardless of age contrasts with the age-related methylation observed in human intestine, suggesting that error accumulation and therefore stem cell latency differs among tissues. Epigenetic molecular clocks imply similar mitotic ages for hairs on young and old human heads, consistent with a restart with each new hair, and with genealogies surreptitiously written within somatic cell genomes.

Biological Principles for Ex Vivo Adult Stem Cell Expansion

Adult stem cells (ASCs) are the engines that drive the renewal of adult mammalian tissues. They divide continuously, throughout life, to produce new progeny cells that undergo a robust development program of differentiation and maturation to replace older expired tissue cells. The same cell turnover program may function to provide limited repair and regeneration of adult tissues in some cases. The regenerative potential of ASCs drives the current intense interest in adapting them for applications in cell replacement therapy. However, research to explore this potential has been blunted by an unyielding biological problem. ASCs have proven highly refractory to expansion of their numbers and long-term propagation in culture. A review of reported strategies to overcome this problem reveals that many studies focus on traditional cell culture factors that may not apply to ASCs and overlook a special property of ASCs that may be universally critical for successful expansion, asymmetric cell kinetics (ACK). This property is reflected by the different kinetics fate of the two sister cells resulting from an ASC division: one cell remains an ASC and keeps the potential to divide for the entire life span of the tissue, while the other cell's progeny eventually differentiates and undergoes terminal division arrest. This unique property of ASCs may prove to be the obligatory factor that must be breached by any method that will succeed in accomplishing routine expansion of ASCs of diverse tissue origin.

Age-related human small intestine methylation: evidence for stem cell niches

BACKGROUND

The small intestine is constructed of many crypts and villi, and mouse studies suggest that each crypt contains multiple stem cells. Very little is known about human small intestines because mouse fate mapping strategies are impractical in humans. However, it is theoretically possible that stem cell histories are inherently written within their genomes. Genomes appear to record histories (as exemplified by use of molecular clocks), and therefore it may be possible to reconstruct somatic cell dynamics from somatic cell errors. Recent human colon studies suggest that random somatic epigenetic errors record stem cell histories (ancestry and total numbers of divisions). Potentially age-related methylation also occurs in human small intestines, which would allow characterization of their stem cells and comparisons with the colon.

METHODS

Methylation patterns in individual crypts from 13 small intestines (17 to 78 years old) were measured by bisulfite sequencing. The methylation patterns were analyzed by a quantitative model to distinguish between immortal or niche stem cell lineages.

RESULTS

Age-related methylation was observed in the human small intestines. Crypt methylation patterns were more consistent with stem cell niches than immortal stem cell lineages. Human large and small intestine crypt niches appeared to have similar stem cell dynamics, but relatively less methylation accumulated with age in the small intestines. There were no apparent stem cell differences between the duodenum and ileum, and stem cell survival did not appear to decline with aging.

CONCLUSION

Crypt niches containing multiple stem cells appear to maintain human small intestines. Crypt niches appear similar in the colon and small intestine, and the small intestinal stem cell mitotic rate is the same as or perhaps slower than that of the colon. Although further studies are needed, age-related methylation appears to record somatic cell histories, and a somatic epigenetic molecular clock strategy may potentially be applied to other human tissues to reconstruct otherwise occult stem cell histories.

A stop-EGFP transgenic mouse to detect clonal cell lineages generated by mutation

The investigation of cell lineages and clonal organization in tissues is facilitated by techniques that allow labelling of clonal cell lineages. Here, we describe a novel transgenic mouse that allows clonal cell lineages to be traced in virtually any tissue. A green fluorescent cell lineage is generated by a random mutation at an enhanced green fluorescent protein gene that carries a premature stop codon, ensuring clonality. The transgenic system allows efficient detection of mutations and stem-cell fate mapping in the epidermis using live mice, as well as in the kidney and liver post-mortem. Cell lineages that descended from single epidermal stem cells were found to be capable of generating three adjacent corneocytes using the system, providing evidence for horizontal migration of epidermal cells between epidermal proliferative units (EPUs), in contrast to the classical EPU model. The transgenic mouse system is expected to provide a novel tool for stem-cell lineage studies.

Tracing ancestry with methylation patterns: most crypts appear distantly related in normal adult human colon

Background

The ability to discern ancestral relationships between individual human colon crypts is limited. Widely separated crypts likely trace their common ancestors to a time around birth, but closely spaced adult crypts may share more recent common ancestors if they frequently divide by fission to form clonal patches. Alternatively, adult crypts may be long-lived structures that infrequently divide or die.

Methods

Methylation patterns (the 5' to 3' order of methylation) at CpG sites that exhibit random changes with aging were measured from isolated crypts by bisulfite genomic sequencing. This epigenetic drift may be used to infer ancestry because recently related crypts should have similar methylation patterns.

Results

Methylation patterns were different between widely separated ("unrelated") crypts greater than 15 cm apart. Evidence for a more recent relationship between directly adjacent or branched crypts could not be found because their methylation pattern distances were not significantly different than widely separated crypt pairs. Methylation patterns are essentially equally different between two adult human crypts regardless of their relative locations.

Conclusions

Methylation patterns appear to record somatic cell trees. Starting from a single cell at conception, sequences replicate and may drift apart. Most adult human colon crypts appear to be long-lived structures that become mosaic with respect to methylation during aging.

Asymmetric cell kinetics genes: the key to expansion of adult stem cells in culture

A singular challenge in stem cell research today is the expansion and propagation of functional adult stem cells. Unlike embryonic stem cells, which are immortal in culture, adult stem cells are notorious for the difficulty encountered when attempts are made to expand them in culture. One overlooked reason for this difficulty may be the inherent asymmetric cell kinetics of stem cells in postnatal somatic tissues. Senescence is the expected fate of a culture whose growth depends on adult stem cells that divide with asymmetric cell kinetics. Therefore, the bioengineering of strategies to expand adult stem cells in culture requires knowledge of cellular mechanisms that control asymmetric cell kinetics. The properties of several genes recently implicated to function in a cellular pathway(s) that regulates asymmetric cell kinetics are discussed. Understanding the function of these genes in asymmetric cell kinetics mechanisms may be the key that unlocks the adult stem cell expansion problem.

Methylation reveals a niche: stem cell succession in human colon crypts

Little it known about human stem cells although they are likely to be the earliest progenitors of carcinomas. Just as methylation can substitute for mutations to inactivate tumor suppressor genes, methylation can also substitute for mutations in a phylogenetic analysis. This review explains why stem cell dynamics may be important to tumor progression and how methylation patterns found in a normal human colon can be used to reconstruct the behavior of crypt stem cells. Histories are recorded in sequences and strategies used to reconstruct phylogenies from sequences likely apply to methylation patterns because both exhibit somatic inheritance. Such a quantitative analysis of colon methylation patterns infers stem cells live in niches containing multiple 'stem' cells. Although niche stem cell numbers remain constant, clonal succession is inherent to niches because periodically progeny from a single stem cell become dominant. These niche succession cycles may potentially accumulate multiple alterations because they resemble superficially the clonal succession of tumor progression except that they occur invisibly in the absence of selection or phenotypic change. Alterations without immediate selective value may hitchhike passively in the stem cells that become dominant during niche succession cycles. The inherent ability of a niche to fix alterations (Muller's ratchet) is another potential mechanism besides instability and selection to sequentially accumulate multiple alterations. Many alterations found in colorectal tumors may reflect such occult clonal progression in normal colon.