Following more than four decades of intense research, scientists may be closer to deciphering the precise mechanisms at work in stem cell development and differentiation, a recent paper published in the Journal of Molecular Endocrinology reports.

Stem cells control organ homeostasis, growth, and self-regulation. This is done by relying on a network of short-range, localized transcription factors (TFs). Transcription factors are a major effector of physiological changes and wield significant influence on stem cell behavior in many ways.

The absence or overexpression of only one transcription factor is enough to affect stem cells differently at various developmental stages.

In this review of the latest research, we will survey how TFs affect embryonic stem cell development and how they interact in adult tissue to establish the stem cell niche, their somatic function, maintenance, and the differentiation process. Because TFs are the major effector of cellular change, such a pivotal role requires a certain versatility in which these factors can operate. The vast complexity of the science and diversity of stem cells be it embryonic or adult (physiological), induced pluripotent (artificially reprogrammed), or cancer, indicates the important role these factors have when responding to environmental cues and certain physiological challenges.

Understanding the innate processes occurring in stem cells is of obvious medical importance. Each notch of progress contained within science reshapes the field of epigenetics and how we, ultimately, think of stem cell morphology and the development of disease.

Transcription Factors: to express or not to express

 Tissue-specific stem cells replace damaged cells and allow for organs to respond to various environmental changes. Accumulating evidence points to a network of transcription factors, which can regulate both the formation and the function of stem cells within their niches. However, a complete understanding of how they interact within developed systems is lacking.

What scientists at the University of Santiago de Compostela (USC) have shown is that transcription factors regulate stem cells on all levels and types and can affect both their maintenance and rate of proliferation. Moreover, all types of stem cells appear to share a set of four main TFs, which ensures a coordinated function and gene regulation throughout life. The four core TFs identified in the study are: OCT4, SOX2, KLF4, and NANOG [1].

Mounting evidence suggests that stem cells maintain pluripotency through a balanced expression of these four coretranscription factors. Together, they also coordinate the expression of second-tier transcription factors (DPP3 or STELLA, REX1 or ZNF42, and GBX2), cell surface markers (SSEA4 in humans or SSEA1 in rodents), ABC transporters (ABCG2), and certain enzymes (alkaline phosphatase and telomerase TERT) [2].

A good working principle in stem cell biology is that one TF can have a profound effect on the development of theembryo. The overexpression or loss of only one TF can throw off the careful balance maintained in an early transcriptional network. When inputs from these are out of balance, a stem cell will systematically become committed, further inducing other physiological changes. Although evidence is still lacking for several niches in adult tissue, it’s known that adult stem cells (ASCs) maintain the expression of three of the four TFs characterized in ESCs (OCT4, KLF4, and SOX2) and have a set of tissue-specific markers dependent upon their niche location [3].

When taken together, a picture emerges in which TFs act as the directors of gene function coordinating the formation of somatic and germ cell lineages. Any shift in balance among these TFs is a cellular cue to switch from a role of proliferation into differentiation [4].

The numerous stem cell systems affected by each TF and the wide range of effects they exert suggest that understanding regulation of stem cells will require a concerted effort in years to come.


Embryonic stem cells (ESCs) are highly specialized and the most functionally diverse collection of cells in organisms. A cascade of signals from the inner cell mass causes the embryo to differentiate into three germ layers of the blastocyst: 1) mesoderm, generating muscle, heart, kidney, cartilage and bone cells and blood-forming tissues, 2) ectoderm, developing the nervous system and giving rise to the epidermis, and 3) endoderm, which will eventually grow into the gut and lungs. As cells develop along each path, they become more and more specialized until they can no longer change.

In order to coordinate gene expression during the differentiation process and maintain the cell in a state of pluripotency, ESCs must balance the expression between four main transcription factors. Should one TF be overexpressed in relation to any of the others, this shift in balance will sway the cell(s) toward a differentiated fate. Various techniques have been used to demonstrate pluripotency in stem cells, but scientists at the University of Santiago de Compostela (USC) found that altering the balance between any one of these transcription factors will cause an ESC to become committed [5].

Table 1 shows a summary of the key mechanisms that maintain pluripotency in ESCs. How stem cell morphology is regulated among these transcription factors is summarized below [6]:

  • The formation of the primitive ectoderm and mesoderm is followed by an increase in FGF5, and a loss of REX1 expression.
  • Either the overexpression of OCT4 and/or the repression of NANOG will sway the cells away from an ectodermal fate and induce differentiation in the endoderm and mesoderm.
  • Over-expression of SOX2 will induce differentiation in the neuro-ectoderm and also repress both OCT4 and REX1.
  • The loss of pluripotency markers OCT4, KLF4, and alkaline phosphatase decrease the self-renewal capacity of ESCs.

Table 1 Mechanisms that maintain pluripotency in ESCs.



Expression of genes characteristic of pluripotency

E.g. OCT4, SOX2, KLF4, REX, telomerase, alkaline phosphatase, ABCG2

Codependence of expression of other core transcription factors to maintain correct levels of expression (no more, no less)

E.g. indirect regulation of OCT4 expression by SOX2

Heterodimerization as a regulator of pluripotency genes

E.g. OCT4/SOX2 heterodimer allows concurrent binding of the two OCT4 DNA-binding domains

Allelic switching

E.g. random transcription from a single allele characteristic of NANOG transcription in non-pluripotent cells. A change from mono- to biallelic expression is exclusive to pluripotent ESCs

Majority of genes maintained in a poised epigenetic state

E.g. general undermethylation of DNA, histones in promoters sharing features both of activation and repression (H3K4Me3 and H3K27Me3)

Specific repression (overmethylation) of a few specific genes

E.g. HLA locus, CDKN1B (p27), and RASSF1

Other epigenetic events

E.g. RNA variants generated through alternative splicing or microRNAs


The Adult Stem Cell Niche

Adult Stem Cells (ASCs) are the cornerstones of tissue renewal, repair, and remodeling in mature organs. They can be divided into one of two groups known either as parenchymal or mesenchymal stem cells, depending on their location. The ability of ASCs to adapt and respond to the needs of tissues is derived, by and large, from their association with the niche. In essence, a niche is a microenvironment capable of maintaining stemness and directs downstream cellular behavior through its relationship with nearby cells (See Figure 1).

ASC.niche(Photo courtesy of Journal of Molecular Endocrinology)

Figure 1 The adult SC niche. ASCs are organized in a compact structure supported by MSCs and receive specific neural (sympathetic) and vascular support. ASCs proliferate slowly, which impartially drives the cells to either remain in the niche or to become progenitors and leave the niche. Random influences such as proximity to cytokines might decide ASC fate through symmetric or asymmetric divisions.

In order to function, stem cells depend on an instructive environment that is composed of signals from neighboring cells, as well as, the extracellular matrix (niche). Within this niche matrix, ASCs are supported, protected, and nurtured by MSCs, where they divide to become parenchymal ASCs, which provides the functional cells required by the entire organ. A myriad of signals, markers, and feedback loops between stem cells, somatic cells and their niches ensure the correct behavior of adult stem cells.

In the bone marrow niche, for example, mesenchymal stem cells (MSCs) are characterized by the expression of CD271 and CD146 markers, as well as, b-adrenergic receptor 3, angiopoietin 1, and the chemokine CXCL12. Subcutaneous and peritoneal fat MSCs express CD29 and CD105 [7]. Hematopoietic SCs (HSCs) will express CXCR4 when stimulated by routine circadian adrenaline [8,9,10]. This last finding, in particular, was the first time any study has demonstrated that the central nervous system (CNS) could regulate a niche via inputs from the peripheral nervous system. But is the communication between cells and their SC niche enough to maintain homeostasis, or is it possible that an extrinsic mechanism is required to sustain each niche, such as signals from the CNS? And do stem cells require active coordination between niches, or does it happen in absence of autonomous regulation? Answers to these questions are still unknown and will be required in the next phase of research.

It is our view that one of the next breakthroughs in stem cell biology will be in determining the higher order processes that coordinate stem cell-niche units for organ tissue.


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