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Regulation of somatic stem cell Function

Posted in Biological Networks, Gene Regulation and Evolution, Chemical Biology and its relations to Metabolic Disease, Genome Biology, Hematology, Hematopoiesis, hNPCs, Human neural progenitor cells, Molecular Genetics & Pharmaceutical, Neurodegenerative Diseases, Personalized and Precision Medicine & Genomic Research, Population Health Management, Genetics & Pharmaceutical, Regenerative Biology and Medicine, Stem Cells for Regenerative Medicine, Translational Research, Translational Science, tagged aging cells, cell lineages, directed differentiation, DNA methylation, epigenetic pathways, Epigenetics, Hematopoietic stem cells, imprinted gene network, iPSCs, Methylation, methylome, multi-lineage differentiation, neural stem cells, Parkinsons disease, self-renewal, somatic stem cells on July 29, 2014| Leave a Comment »

Writer and curator: Larry H. Bernstein, MD, FCAP and
Curator: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013-01-23/larryhbern/Regulation-of-somatic-stem-cell-function/

There is an explosion of work-in-progress in applications to regenerative medicine using inducible pluripotent stem cells in both endothelial and cardiomyocyte postischemic repair, and also in post bone marrow radiation restoration, with benefits and hazards. The following article is quite novel in that it deals with stem cell regulation by DNA methylation. Therefore, it deals with the essentiality of methylation of DNA in epigenetic regulation.

This is the fourth discussion of a several part series leading from the genome, to protein synthesis (1), posttranslational modification of proteins (2), examples of protein effects on metabolism and signaling pathways (3), and leading to disruption of signaling pathways in disease (4), and effects leading to mutagenesis.

1. A Primer on DNAand DNA Replication

http://pharmaceuticalintelligence.com/2014-28-07/A_Primer_on_DNA_and_DNA_Replication

2. Overview of translational medicine

http://pharmaceuticalintelligence.com/2014-07-28/larryhbern/overview-of-posttranslational-medicine

3. Genes, proteomes, and their interaction

http://pharmaceuticalintelligence.com/7/17/2014/Genes, proteomes, and their interaction

4. Regulation of somatic stem cell Function

http://pharmaceuticalintelligence.com/2013-01-23/larryhbern/Regulation-of-somatic-stem-cell-function/

5. Proteomics – The Pathway to Understanding and Decision-making in Medicine

http://pharmaceuticalintelligence.com/2014/06/24/proteomics-the-pathway-to-understanding-and-decision-making-in-medicine/

6. Genomics, Proteomics and standards

http://pharmaceuticalintelligence.com/2014/07/06/genomics-proteomics-and-standards/

7. Long Non-coding RNAs Can Encode Proteins After All

8. Proteins and cellular adaptation to stress

http://pharmaceuticalintelligence.com/2014/07/08/proteins-and-cellular-adaptation-to-stress/

9. Loss of normal growth regulation

http://pharmaceuticalintelligence.com/2014/07/06/loss-of-normal-growth-regulation/

Posttranslational modification is a step in protein biosynthesis. Proteins are created by ribosomes translating mRNA into polypeptide chains. These polypeptide chains undergo
PTM before becoming the mature protein product.

Regulation of somatic stem cell Function by DNA Methylation and Genomic Imprinting

Mo Li1, Na Young Kim1, Shigeo Masuda1 and Juan Carlos izpisua Belmonte1,2 1Salk institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA. 2Center of Regenerative Medicine in Barcelona, Dr Aiguader, 88, 08003 Barcelona, Spain. Corresponding author email: mli@salk.edu

Cell & Tissue Transplantation & Therapy 2013:5 19–23
http://dx.doi.org/10.4137/CTTT.S12142
This article is available from http://www.la-press.com

Abstract:

Epigenetic regulation is essential for self-renewal and differentiation of somatic stem cells, including

hematopoietic stem cells (HSCs) and
neural stem cells (NSCs).

The role of DNA methylation, a key epigenetic pathway,

in regulating somatic stem cell function
- under physiological conditions and during aging

has been intensively investigated.

Accumulating evidence highlights the dynamic nature of

the DNAmethylome
- during lineage commitment of somatic stem cells and
the pivotal role of DNAmethyltransferases in
- stem cell self-renewal and differentiation.

Recent studies on genomic imprinting have shed light on

the imprinted gene network (IGN) in somatic stem cells,

where a subset of imprinted genes remain expressed and
are important for maintaining self-renewal of these cells.

Together with emerging technologies, elucidation of the epigenetic mechanisms regulating somatic stem cells with normal or pathological functions may contribute to the development of regenerative medicine.

Keywords: somatic stem cells, epigenetics, DNA methylation, genomic imprinting, hematopoietic stem cells, neural stem cells

Introduction

In adult animals, somatic stem cells (also known as adult stem cells) are responsible for maintaining tissue homeostasis and participate in tissue regeneration under injury conditions. Self-renewal and differentiation are two important aspects of somatic stem cell function. Epigenetic mechanisms underlying these processes have been intensively investigated. With the increasing ability

to identify and manipulate somatic stem cell populations from diverse tissues,
it is possible to dissect the epigenetic pathways that are

either unique for a specific tissue or
universally important in regulating stemness and differentiation.

Epigenetic control of somatic stem cell function exists at various levels, including

DNA methylation,
histone modification, and
higher-order chromatin structure dynamics.

Here, we focus on recent progress in our understanding of how

DNA methylation regulates somatic stem cell function.

DNA Methylation and stem cell Function

The role of DNA methylation in somatic stem cell compartments has gained increasing attention. Recent evidence has shown that

DNA methylation is dynamically regulated during somatic stem cell differentiation and aging.1

A study of methylomes of human hematopoietic stem cells (HSCs) and two mature hematopoietic lineages,

including B cells and neutrophils, showed that
- hypomethylated regions of lineage-specific genes often become methylated in opposing lineages, and that
- progenitors display an intermediate methylation pattern

that is poised for lineage-specific resolution.2

Another study compared genome-wide promoter DNA methylation in human cord blood hematopoietic progenitor cells (HPCs) with

that in mobilized peripheral blood HPCs from aged individuals.

It was found that aged HPCs lose DNA methylation in a subset of genes that are hypomethylated in differentiated myeloid cells and

gain de novo DNA methylation at polycomb repressive complex 2 (PRC2) target sites.3

It was hypothesized that such epigenetic changes contribute to age-related loss of HSC function, such as a bias toward myeloid lineages. Recently, Beerman et al. studied the global DNA methylation landscape of HSCs in the context of

age-associated decline of HSC function.4

Over- all, the DNA methylation landscape remains stable during HSC ontogeny. However, HSCs isolated from old mice display higher global DNA methylation. Interestingly, they observed

localized DNA methylation changes in genomic regions associated with hematopoietic lineage differentiation.

These methylation changes preferentially map to genes

that are expressed in downstream progenitor and effector cells.

For example, genes that are important for the lymphoid and erythroid lineages

become methylated in “old” HSCs,

which is consistent with

the decline of lymphopoiesis and erythropoiesis during aging.

Additionally, inducing HSC proliferation by 5-fluorouracil treatment or

by limiting the number of transplantedHSCs
- recapitulates the functional decline and DNA methylation changes during physiological aging.

A closer examination of the overlapping genes with significant DNA methylation changes during aging or enforced proliferation showed

an enrichment of DNA hypermethylation at PRC2 target loci,

echoing the observation by Bocker et al. in human HSCs.

Interestingly, a recent report showed that epigenetic alterations such as DNA hypermethylation that are accrued during aging,

can be fully reset by somatic reprogramming,

raising an interesting possibility that these aging-related epigenetic defects may be reserved by small molecules.5

Methylation of cytosines at CpG dinucleotides is catalyzed by three key enzymes.

DNA (cytosine-5)- methyltransferase 1 (DNMT1) is responsible for maintaining DNA methylation patterns during DNA replication

by methylating the newly synthesized hemi-methylated DNA.

The other two DNA methyltransferases, DNMT3a and DNMT3b,

are not DNA replication-dependent and can methylate fully unmethylated DNA de novo.

They are responsible for establishing new DNA methylation patterns during development.

DNMT3a, a gene required for neurogenesis,

is expressed in postnatal neural stem cells (NSCs).

In NSCs, DNMT3a methylates non-proximal promoter regions, such as gene bodies and intergenic regions. Surprisingly, rather than silencing gene expression,

DNMT3a-mediated DNA methylation in gene bodies antagonizes Polycomb-dependent repression and

facilitates the expression of neurogenic genes.6

The role of DNMT3a in HSCs has also been investigated. Both Dnmt3a and Dnmt3b are expressed in HSCs. An earlier study did not identify any defects in HSC function when Dnmt3a or Dnmt3b was removed. However,

HSCs lackingboth of these de novomethyltransferases
- fail to self-renew, yet retain the capacity to differentiate.7

A more recent study re-examined

the consequences of Dnmt3a loss in HSCs and
uncovered a progressive defect in differentiation that is only manifested during serial transplantation.8

At the molecular level, while Dnmt3a loss results in the expected hypomethylation at some loci,

it counterintuitively causes hypermethylation in even more regions.8

This seemingly paradoxical result echoes the unconventional role of Dnmt3a in transcriptional activation in NSCs (as discussed above). Both cases suggest a more complex regulatory function of DNMT3a that is

beyond simply methylating DNA.

In contrast, the loss of Dnmt1 produces more dramatic and immediate phenotypes in HSCs, manifested

in premature HSC exhaustion and
block of lymphoid differentiation,

highlighting the distinct requirements for different DNA methyltransferases in HSCs.9,10

Genomic Imprinting and stemness

DNA methylation also underlies genomic imprinting, which is an

evolutionarily conserved epigenetic mechanism of ensuring appropriate gene dosage during development.

One allele of the imprinted genes is

epigenetically marked by DNA methylation to be silenced according to the parental origin.

The pattern of imprinting

is established in germ cells and maintained in somatic cells.

Imprinted genes are thought to play critical roles in organismal growth and are relatively downregulated after birth.11 Recently, a series of reports demonstrated that

a subset of imprinted genes belonging to the purported imprinted gene network (IGN)12
remain expressed in somatic stem cells and
are important for maintaining self-renewal of these cells.

Through gene expression profiling, one group identified that several members of the IGN are expressed in

murine muscle,
epidermal, and
long-term hematopoietic stem cells
as well as in human epidermal and hematopoietic stem cells.13

In particular, the paternally expressed gene 3 (Peg3) gene was shown by another group

to mark cycling and quiescent stem cells in a wide variety of mouse tissues.14

The role of imprinted genes in regulating somatic stem cell function has been examined in two types of tissues.

In bronchioalveolar stem cells (BASCs), a lung epithelial stem cell population,

expression of IGN members is required for their self-renewal.

Bmi1, a polycomb repressive complex 1 (PRC1) subunit,

is essential for controlling the expression of imprinted genes in BASCs without affecting their imprinting status.15

In Bmi1 mutant BASCs, many members of the IGN become derepressed,

including p57, H19, Dlk1, Peg3, Ndn, Mest, Gtl2, Grb10, Plagl1, and Igf2.

Knockdown of p57, which is the most differentially expressed imprinted gene between normal and mutant BASCs,

partially rescues the self-renewal defect of lung stem cells.

Interestingly, insufficient levels of p57 also inhibit self-renewal of lung stem cells. Because p57 expression

remains monoallelic in Bmi1 knockdown cells,
Bmi1 is thought to maintain an appropriate level of expression from the expressed allele of p57.15

Another IGN member- delta-like homologue 1 (Dlk1) has been shown to be important for postnatal neurogenesis. Interestingly, in this context,

Dlk1 loses its imprinting in postnatal neural stem cells and niche astrocytes.16

These studies suggest that modulating IGN may represent another

epigenetic mechanism for balancing self-renewal and differentiation in somatic stem cells.

Thus, somatic stem cells either co-opt or remodel these developmental pathways involving the IGN

to fulfill the needs of tissue homeostasis during the adult stage.

In summary, several factors participate in regulating the epigenome of somatic stem cells.

Perturbations in the epigenome of somatic stem cells,

either during organismal aging or under pathological conditions,

will tip the balance between self-renewal and differentiation of somatic stem cells (Fig. 1). A detailed understanding of the mechanisms underlying these changes will likely result in novel therapeutic approaches targeting somatic stem cells.

Figure 1. The epigenome of somatic stem cells is regulated by diverse factors.

Future perspectives The epigenetic mechanisms governing self-renewal and differentiation of somatic stem cells are likely to be complex because of the diverse needs of different tissues. It would be interesting to determine whether a common mechanism, such as the IGN, exists across different somatic stem cells. Additionally, study- ing epigenetic pathways that are specific to one type of somatic stem cell requires the isolation of these cells and their differentiated progeny, which is more practical in model organisms than in humans. Along these lines, developing robust in vitro culture methods for human somatic stem cells and protocols for differentiating these cells into specific lineages are critical for uncovering epigenetic pathways that are unique to human somatic stem cells. In recent years, the field has seen a great improvement in methods of directed differentiation of human embryonic stem cells and induced pluripotent stem cells (iPSCs). For example, it is relatively straightforward to produce high-purity cell populations that resemble neural stem cells or mesenchymal stem cells from iPSCs.17

These methodologies not only are useful for studying the normal function of somatic stem cells, but also provide an exciting opportunity for understanding the role of somatic stem cells in disease pathology and a platform to screen for drugs. A recent study under- scored the usefulness of this approach. Liu et al. studied neural stem cells derived from Parkinson’s disease human iPSCs and uncovered previously unknown defects in nuclear morphology and epigenetic regulation in these derived NSCs.18 The cellular defects only menifest in “aged” neural stem cells, which is consistent with the fact that Parkinson’s disease pri- marily manifests in old age. More importantly, this study identified neural stem cell as a potential target of therapeutic intervention for Parkinson’s disease.

Targeted modification of the human genome is another technological advancement that is on the horizon to greatly facilitate the dissection of epige- netic pathways in somatic stem cells. Although gene targeting in somatic stem cells has been historically challenging, there have been encouraging successful reports following development of new genome-e diting technologies, such as Helper-dependent adenovi- ral vectors, TALENs, and CAS9/CRISPR. With the development of these new technologies, it seems that the stage has been set for a new wave of discoveries in epigenetic mechanisms of somatic stem cells.

References

1. Li M, Liu GH, Izpisua Belmonte JC. Navigating the epigenetic landscape of pluripotent stem cells. Nat Rev Mol Cell Biol. 2012;13(8):524–535.

2. Hodges E, Molaro A, Dos Santos CO, et al. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell. 2011;44(1):17–28.

3. Bocker MT, Hellwig I, Breiling A, Eckstein V, Ho AD, Lyko F. Genome- wide promoter DNA methylation dynamics of human hematopoietic progen- itor cells during differentiation and aging. Blood. 2011;117(19):e182–e189.

4. Beerman I, Bock C, Garrison BS, et al. Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging. Cell Stem Cell. 2013;12(4):413–425.

5. Wahlestedt M, Norddahl GL, Sten G, et al. An epigenetic component of hematopoietic stem cell aging amenable to reprogramming into a young state. Blood. 2013;121(21):4257–4264.

6. Wu H, Coskun V, Tao J, et al. Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science. 2010; 329(5990):444–448.

7. Tadokoro Y, Ema H, Okano M, Li E, Nakauchi H. De novo DNA meth- yltransferase is essential for self-renewal, but not for differentiation, in hematopoietic stem cells. J Exp Med. 2007;204(4):715–722.

8. Challen GA, Sun D, Jeong M, et al. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet. 2011;44(1):23–31.

9. Broske AM, Vockentanz L, Kharazi S, et al. DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nat Genet. 2009;41(11):1207–1215.

10. Trowbridge JJ, Snow JW, Kim J, Orkin SH. DNA methyltransferase 1 is essential for and uniquely regulates hematopoietic stem and progenitor cells. Cell Stem Cell. 2009;5(4):442–449.

11. Wood AJ, Oakey RJ. Genomic imprinting in mammals: emerging themes and established theories. PLoS Genet. 2006;2(11):e147.

12. Lui JC, Finkielstain GP, Barnes KM, Baron J. An imprinted gene network that controls mammalian somatic growth is down-regulated during postna- tal growth deceleration in multiple organs. Am J Physiol Regul Integr Comp Physiol. 2008;295(1):R189–R196.

13. Berg JS, Lin KK, Sonnet C, et al. Imprinted genes that regulate early mam- malian growth are coexpressed in somatic stem cells. PLoS One. 2011; 6(10):e26410.

14. Besson V, Smeriglio P, Wegener A, et al. PW1 gene/paternally expressed gene 3 (PW1/Peg3) identifies multiple adult stem and progenitor cell popu- lations. Proc Natl Acad Sci U S A. 2011;108(28):11470–11475.

15. Zacharek SJ, Fillmore CM, Lau AN, et al. Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci. Cell Stem Cell. 2011;9(3):272–281.

16. Ferron SR, Charalambous M, Radford E, et al. Postnatal loss of Dlk1 imprinting in stem cells and niche astrocytes regulates neurogenesis. Nature. 2011;475(7356):381–385.

17. Li W, Sun W, Zhang Y, et al. Rapid induction and long-term self-renewal of primitive neural precursors from human embryonic stem cells by small molecule inhibitors. Proc Natl Acad Sci U S A. 2011;108(20):8299–8304.

18. Liu GH, Qu J, Suzuki K, et al. Progressive degeneration of human neural stem cells caused by pathogenic LRRK2. Nature. 2012;491(7425):603–607.

Additional References in Leaders in Pharmaceutical Intelligence

Proteomics and Biomarker Discovery

http://pharmaceuticalintelligence.com/2012/08/21/proteomics-and-biomarker-discovery/

Developments in the Genomics and Proteomics of Type 2 Diabetes Mellitus and Treatment Targets

http://pharmaceuticalintelligence.com/2013/12/08/developments-in-the-genomics-and-proteomics-of-type-2-diabetes-mellitus-and-treatment-targets/

Immune activation, immunity, antibacterial activity

http://pharmaceuticalintelligence.com/2014/07/06/immune-activation-immunity-antibacterial-activity/

Ubiquitin-Proteosome pathway, Autophagy, the Mitochondrion, Proteolysis and Cell Apoptosis: Part III

http://pharmaceuticalintelligence.com/2013/02/14/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion-proteolysis-and-cell-apoptosis-reconsidered/

Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

http://pharmaceuticalintelligence.com/2012/10/30/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion-proteolysis-and-cell-apoptosis/