Chromatin, epigenetics and stem cells

Above the Epitranscriptome: RNA Modifications and Stem Cell Identity

Sequence databases and transcriptome-wide mapping have revealed different reversible and dynamic chemical modifications of the nitrogen bases of RNA molecules. Modifications occur in coding RNAs and noncoding-RNAs post-transcriptionally and they can influence the RNA structure, metabolism, and function. The result is the expansion of the variety of the transcriptome. In fact, depending on the type of modification, RNA molecules enter into a specific program exerting the role of the player or/and the target in biological and pathological processes. Many research groups are exploring the role of RNA modifications (alias epitranscriptome) in cell proliferation, survival, and in more specialized activities. More recently, the role of RNA modifications has been also explored in stem cell biology. Our understanding in this context is still in its infancy. Available evidence addresses the role of RNA modifications in self-renewal, commitment, and differentiation processes of stem cells. In this review, we will focus on five epitranscriptomic marks: N6-methyladenosine, N1-methyladenosine, 5-methylcytosine, Pseudouridine (Ψ) and Adenosine-to-Inosine editing. We will provide insights into the function and the distribution of these chemical modifications in coding RNAs and noncoding-RNAs. Mainly, we will emphasize the role of epitranscriptomic mechanisms in the biology of naïve, primed, embryonic, adult, and cancer stem cells.

Methyl-CpG binding domain proteins inhibit interspecies courtship and promote aggression in Drosophila

Reproductive isolation and speciation are driven by the convergence of environmental and genetic variation. The integration of these variation sources is thought to occur through epigenetic marks including DNA methylation. Proteins containing a methyl-CpG-binding domain (MBD) bind methylated DNA and interpret epigenetic marks, providing a dynamic yet evolutionarily adapted cellular output. Here, we report the Drosophila MBD-containing proteins, dMBD-R2 and dMBD2/3, contribute to reproductive isolation and survival behavioral strategies. Drosophila melanogaster males with a reduction in dMBD-R2 specifically in octopamine (OA) neurons exhibit courtship toward divergent interspecies D. virilis and D. yakuba females and a decrease in conspecific mating success. Conspecific male-male courtship is increased between dMBD-R2-deficient males while aggression is reduced. These changes in adaptive behavior are separable as males with a hypermethylated OA neuronal genome exhibited a decrease in aggression without altering male-male courtship. These results suggest Drosophila MBD-containing proteins are required within the OA neural circuitry to inhibit interspecies and conspecific male-male courtship and indicate that the genetically hard-wired neural mechanisms enforcing behavioral reproductive isolation include the interpretation of the epigenome.

Epigenetics in heart failure phenotypes

Chronic heart failure (HF) is a leading clinical and public problem posing a higher risk of morbidity and mortality in different populations. HF appears to be in both phenotypic forms: HF with reduced left ventricular ejection fraction (HFrEF) and HF with preserved left ventricular ejection fraction (HFpEF). Although both HF phenotypes can be distinguished through clinical features, co-morbidity status, prediction score, and treatment, the clinical outcomes in patients with HFrEF and HFpEF are similar. In this context, investigation of various molecular and cellular mechanisms leading to the development and progression of both HF phenotypes is very important. There is emerging evidence that epigenetic regulation may have a clue in the pathogenesis of HF. This review represents current available evidence regarding the implication of epigenetic modifications in the development of different HF phenotypes and perspectives of epigenetic-based therapies of HF.

The functional role of long non-coding RNAs and epigenetics

Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, involving in diverse cellular processes. The regulation of gene expression by lncRNAs at the epigenetic level, transcriptional and post-transcriptional level have been well known and widely studied. Recent recognition that lncRNAs make effects in many biological and pathological processes such as stem cell pluripotency, neurogenesis, oncogenesis and etc. This review will focus on the functional roles of lncRNAs in epigenetics and related research progress will be summarized.

NCBI Epigenomics: what's new for 2013

The Epigenomics resource at the National Center for Biotechnology Information (NCBI) has been created to serve as a comprehensive public repository for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). We have constructed this resource by selecting the subset of epigenetics-specific data from the Gene Expression Omnibus (GEO) database and then subjecting them to further review and annotation. Associated data tracks can be viewed using popular genome browsers or downloaded for local analysis. We have performed extensive user testing throughout the development of this resource, and new features and improvements are continuously being implemented based on the results. We have made substantial usability improvements to user interfaces, enhanced functionality, made identification of data tracks of interest easier and created new tools for preliminary data analyses. Additionally, we have made efforts to enhance the integration between the Epigenomics resource and other NCBI databases, including the Gene database and PubMed. Data holdings have also increased dramatically since the initial publication describing the NCBI Epigenomics resource and currently consist of >3700 viewable and downloadable data tracks from 955 biological sources encompassing five well-studied species. This updated manuscript highlights these changes and improvements.

Prostate cancer stem cells: are they androgen-responsive?

The prostate gland is highly dependent on androgens for its development, growth and function. Consequently, the prostatic epithelium predominantly consists of androgen-dependent luminal cells, which express the androgen receptor at high levels. In contrast, androgens are not required for the survival of the androgen-responsive, but androgen-independent, basal compartment in which stem cells reside. Basal and luminal cells are linked in a hierarchical pathway, which most probably exists as a continuum with different stages of phenotypic change. Prostate cancer is also characterised by heterogeneity, which is reflected in its response to treatment. The putative androgen receptor negative cancer stem cell (CSC) is likely to form a resistant core after most androgen-based therapies, contributing to the evolution of castration-resistant disease. The development of CSC-targeted therapies is now of crucial importance and identifying the phenotypic differences between CSCs and both their progeny will be key in this process.

The combination of valproic acid and lithium delays hematopoietic stem/progenitor cell differentiation

Despite increasing knowledge on the regulation of hematopoietic stem/progenitor cell (HSPC) self-renewal and differentiation, in vitro control of stem cell fate decisions has been difficult. The ability to inhibit HSPC commitment in culture may be of benefit to cell therapy protocols. Small molecules can serve as tools to manipulate cell fate decisions. Here, we tested 2 small molecules, valproic acid (VPA) and lithium (Li), to inhibit differentiation. HSPCs exposed to VPA and Li during differentiation-inducing culture preserved an immature cell phenotype, provided radioprotection to lethally irradiated recipients, and enhanced in vivo repopulating potential. Anti-differentiation effects of VPA and Li were observed also at the level of committed progenitors, where VPA re-activated replating activity of common myeloid progenitor and granulocyte macrophage progenitor cells. Furthermore, VPA and Li synergistically preserved expression of stem cell-related genes and repressed genes involved in differentiation. Target genes were collectively co-regulated during normal hematopoietic differentiation. In addition, transcription factor networks were identified as possible primary regulators. Our results show that the combination of VPA and Li potently delays differentiation at the biologic and molecular levels and provide evidence to suggest that combinatorial screening of chemical compounds may uncover possible additive/synergistic effects to modulate stem cell fate decisions.

Mosquito genomics: progress and challenges

The whole-genome sequencing of mosquitoes has facilitated our understanding of fundamental biological processes at their basic molecular levels and holds potential for application to mosquito control and prevention of mosquito-borne disease transmission. Draft genome sequences are available for Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus. Collectively, these represent the major vectors of African malaria, dengue fever and yellow fever viruses, and lymphatic filariasis, respectively. Rapid advances in genome technologies have revealed detailed information on genome architecture as well as phenotype-specific transcriptomics and proteomics. These resources allow for detailed comparative analyses within and across populations as well as species. Next-generation sequencing technologies will likely promote a proliferation of genome sequences for additional mosquito species as well as for individual insects. Here we review the current status of genome research in mosquitoes and identify potential areas for further investigations.

NO points to epigenetics in vascular development

Our understanding of epigenetic mechanisms important for embryonic vascular development and cardiovascular differentiation is still in its infancy. Although molecular analyses, including massive genome sequencing and/or in vitro/in vivo targeting of specific gene sets, has led to the identification of multiple factors involved in stemness maintenance or in the early processes of embryonic layers specification, very little is known about the epigenetic commitment to cardiovascular lineages. The object of this review will be to outline the state of the art in this field and trace the perspective therapeutic consequences of studies aimed at elucidating fundamental epigenetic networks. Special attention will be paid to the emerging role of nitric oxide in this field.

NCBI Epigenomics: a new public resource for exploring epigenomic data sets

The Epigenomics database at the National Center for Biotechnology Information (NCBI) is a new resource that has been created to serve as a comprehensive public resource for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). Epigenetics is the study of stable and heritable changes in gene expression that occur independently of the primary DNA sequence. Epigenetic mechanisms include post-translational modifications of histones, DNA methylation, chromatin conformation and non-coding RNAs. It has been observed that misregulation of epigenetic processes has been associated with human disease. We have constructed the new resource by selecting the subset of epigenetics-specific data from general-purpose archives, such as the Gene Expression Omnibus, and Sequence Read Archives, and then subjecting them to further review, annotation and reorganization. Raw data is processed and mapped to genomic coordinates to generate 'tracks' that are a visual representation of the data. These data tracks can be viewed using popular genome browsers or downloaded for local analysis. The Epigenomics resource also provides the user with a unique interface that allows for intuitive browsing and searching of data sets based on biological attributes. Currently, there are 69 studies, 337 samples and over 1100 data tracks from five well-studied species that are viewable and downloadable in Epigenomics.

Epigenetics: origins and implications for cancer epidemiology

This paper provides information on the evolution of the 'epigenetics' concept since Aristotle and draws attention to the importance of epigenetic implications for cancer epidemiology in the years to come. Clearly, to understand origins of the concept of epigenetics, it is worthwhile to consider historical arguments associated with evolution. Equally clearly, in the last half of the 20th century, great advances in the understanding of epigenetics and, more specifically, great advances in the understanding of epigenetics in cancer have been made. However, reaping the full benefits of epigenetics lies beyond the predominant experimental studies of today. In general, epigenetics opens many doors in the field of cancer, but it also adds another level of complex, inter-related, and multi-dimensional information to research, and to its interpretation. Overall, future cancer studies should consider, or at least be sensitive to, epigenetic effects and mechanisms. Moving the focus beyond 'pristine' inheritance via DNA alone, cancer epidemiology investigating epigenetic exposures such as environmental factors (exposure to heavy metals, air pollution, arsenic and other toxins), dietary patterns (starvation, famine, contamination), and lifestyle habits (smoking, level of physical activity, and BMI) in populations has the prospect to significantly benefit future cancer prevention and treatment schemes.

Mesenchymal stroma cells improve hyperglycemia and insulin deficiency in the diabetic porcine pancreatic microenvironment

BACKGROUND

Stem cell differentiation is controlled by extracellular cues from the environment and by intrinsic genetic programs within the stem cell. The present study aimed to explore whether mesenchymal stromal cells (MSC) could improve hyperglycemia and insulin production in the diabetic microenvironment.

METHODS

We transplanted male porcine bone marrow-derived EGFP-expressing MSC directly into female diabetic porcine pancreas by multi-point injection. Enzyme-linked immunosorbent assay (ELISA) and fluorescent immunohistochemistry were used to analyze recipients' sera and pancreas tissues for assessment of the therapeutic effect.

RESULTS

Blood glucose levels decreased gradually in MSC-treated recipients from 15 days after the transplantation compared with untreated diabetic controls (15.94+/-0.31 mmol/L versus 16.66+/-0.11 mmol/L; P=0.01). Blood insulin increased and glucagons decreased notably in recipients from 2 weeks post-transplantation compared with untreated diabetic controls (0.049+/-0.004 microg/L versus 0.037+/-0.02 microg/L and 392.9+/-20.3 ng/L versus 433.1+/-27.6 ng/L). Hematoxylin and eosin (HE)-stained sections demonstrated that the number of islets from each section was markedly increased in recipients compared with that of diabetic controls (10.9+/-2.2 versus 4.6+/-1.4; P<0.05) and similar to that of normal controls (10.9+/-2.2 versus 12.6+/-2.6; P>0.05). The newly formed islets were smaller than normal islets (47.2+/-19.6 microm versus 119.6+/-27.7 microm; P<0.05). Analysis of pancreatic sections for EGFP in recipients indicated that the transplanted MSC survived within the pancreas. Insulin immunoreactivity of pancreatic islets showed that the newly formed islets expressed insulin.

DISCUSSION

MSC could improve diabetes upon pancreatic microenvironment without obvious immune rejections. This has theoretical and clinical applications.

Mesenchymal stem cells adopt beta-cell fate upon diabetic pancreatic microenvironment

OBJECTIVES

: This study observed whether mesenchymal stem cells (MSCs) adopt beta-cell fate upon diabetic microenvironment.

METHODS

: We transplanted male porcine MSCs to diabetic female pigs by directly injecting into pancreas. Recipients' sera and pancreatic tissue were analyzed to assess the therapeutic effect. Islets were collected from the sections using laser-capture microdissection. The RNAs from these specimens were extracted and analyzed for insulin and pancreas duodenum homeobox 1 messenger RNA (mRNA) expression. SRY gene was detected from the specimens.

RESULTS

: Compared with untreated diabetic controls, blood glucose level decreased greatly in recipients from 18 days (15.44 +/- 0.31 mmol/L vs 16.66 +/- 0.11 mmol/L) and insulin increased from 14 days (0.048 +/- 0.006 U/L vs 0.030 +/- 0.004 U/L). Hematoxylin and eosin-stained sections demonstrated increased islets in recipients and few lymphocytes present. The newly formed islets were smaller than normal islets (47.2 mum +/- 19.6 vs 119.6 +/- 27.7 mum). Reverse transcription-polymerase chain reaction showed that microdissected cells expressed insulin and pancreas duodenum homeobox 1 mRNA (79.3% +/- 16.2% of control, 65.2% +/- 14.8% of control, respectively). Immunoreactivity showed that the transplanted MSCs expressed insulin. SRY gene and insulin mRNA double-positive cells were found in microdissected cells by fluorescence in situ hybridization.

CONCLUSIONS

This study shows that MSCs could adopt beta-cell fate in diabetic pancreatic microenvironment without obvious immune rejections. Stem cell transplantation in orthotope is a promising therapy for diabetes.

Mesenchymal stem cells contribute to insulin-producing cells upon microenvironmental manipulation in vitro

BACKGROUND

Extracellular microenvironment and intrinsic genetic programs determine the fate of stem cells. We observed whether mesenchymal stem cells (MSCs) contributed to insulin-producing cells in a manipulated microenvironment.

METHODS

We delivered pancreatic pieces into Niobium-Coated Dynamatrix to construct a simulated pancreatic microenvironment, upon which soluble cytokine exchange and direct cell-cell contact between MSCs and pancreatic cells could occur. Bone marrow-derived MSCs were cultured upon the microenvironment. Differentiated isletlike cells were observed under an inverted microscope. Insulin in supernates was measurement by enzyme-linked immunosorbent assay. Insulin and c-peptide expression were verified by fluorescent immunocytochemistry and fluorescence in situ hybridization. Apoptosis of isletlike masses in high-glucose DMEM was detected by FACS.

RESULTS

After 3 to 4 weeks in culture, typical isletlike masses were observed. Insulin secreted by differentiated cells (414.47+/-30.30 mIU/L) was much greater than that of undifferentiated cells (4.89+/-1.01 mIU/L; P<.05). Insulin and c-peptide expression were positive both in protein and mRNA levels. The transdifferentiated isletlike mass did not undergo apoptosis after another 3 weeks of culture in high-glucose DMEM.

CONCLUSION

This simulated injury microenvironment without induction guided MSCs to functional isletlike cells hopefully to replace beta cells.

Epigenetics and neural stem cell commitment

Neural stem cell is presently the research hotspot in neuroscience. Recent progress indicates that epigenetic modulation is closely related to the self-renewal and differentiation of neural stem cell. Epigenetics refer to the study of mitotical/meiotical heritage changes in gene function that cannot be explained by changes in the DNA sequence. Major epigenetic mechanisms include DNA methylation, histone modification, chromatin remodeling, genomic imprinting, and non-coding RNA. In this review, we focus on the new insights into the epigenetic mechanism for neural stem cells fate.

Systems biology and cancer stem cells

The identification, purification and characterization of cancer stem cells (CSCs) holds tremendous promise for improving the treatment of cancer. Mounting evidence is demonstrating that only certain tumour cells (i.e. the CSCs) can give rise to tumours when injected and that these purified cell populations generate heterogeneous tumours. While the cell of origin is still not determined definitively, specific molecular markers for populations containing these CSCs have been found for leukaemia, brain cancer and breast cancer, among others. Systems approaches, particularly molecular profiling, have proven to be of great utility for cancer diagnosis and characterization. These approaches also hold significant promise for identifying distinctive properties of the CSCs, and progress is already being made.

The human insulin gene displays transcriptionally active epigenetic marks in islet-derived mesenchymal precursor cells in the absence of insulin expression

Human islet-derived precursor cells (hIPCs), mesenchymal cells derived in vitro from adult pancreas, proliferate freely and do not express insulin but can be differentiated to epithelial cells that express insulin. hIPCs have been studied with the goal of obtaining large quantities of insulin-producing cells suitable for transplantation into patients suffering from type 1 diabetes. It appeared that undifferentiated hIPCs are "committed" to a pancreatic endocrine phenotype through multiple cell divisions, suggesting that epigenetic modifications at the insulin locus could be responsible. We determined patterns of histone modifications over the insulin gene in human islets and hIPCs and compared them with HeLa and human bone marrow-derived mesenchymal stem cells (hBM-MSCs), neither of which expresses insulin. The insulin gene in islets displays high levels of histone modifications (H4 hyperacetylation and dimethylation of H3 lysine 4) typical of active genes. These are not present in HeLa and hBM-MSCs, which instead have elevated levels of H3 lysine 9 dimethylation, a mark of inactive genes. hIPCs, in contrast, show significant levels of active chromatin modifications, as much as half those seen in islets, and show no measurable H3 K9 methylation. Cells expanded from a minor population of mesenchymal stromal cells found in islets exhibit the same histone modifications as established hIPCs. We conclude that hIPCs, which do not express the insulin gene, nonetheless uniquely exhibit epigenetic marks that could poise them for activation of insulin expression. This epigenetic signature may be a general mechanism whereby tissue-derived precursor cells are committed to a distinct specification. Disclosure of potential conflicts of interest is found at the end of this article.

Epigenetics and the plasticity of differentiation in normal and cancer stem cells

Embryonic stem cells are characterized by their differentiation to all cell types during embryogenesis. In adult life, different tissues also have somatic stem cells, called adult stem cells, which in specific niches can undergo multipotent differentiation. The use of these adult stem cells has considerable therapeutic potential for the regeneration of damaged tissues. In both embryonic and adult stem cells, differentiation is controlled by epigenetic mechanisms, and the plasticity of differentiation in these cells is associated with transcription accessibility for genes expressed in different normal tissues. Abnormalities in genetic and/or epigenetic controls can lead to development of cancer, which is maintained by self-renewing cancer stem cells. Although the genetic abnormalities produce defects in growth and differentiation in cancer stem cells, these cells have not always lost the ability to undergo differentiation through epigenetic changes that by-pass the genomic abnormalities, thus creating the basis for differentiation therapy. Like normal stem cells, cancer stem cells can show plasticity for differentiation. This plasticity of cancer stem cells is also associated with transcription accessibility for genes that are normally expressed in different tissues, including tissues other than those from which the cancers originated. This broad transcription accessibility can also contribute to the behavior of cancer cells by overexpressing genes that promote cell viability, growth and metastasis.

In vivo association of CReMM/CHD9 with promoters in osteogenic cells

Molecular mechanisms that control cell differentiation involve with chromatin remodeling activities. We recently identified Chromatin Related Mesenchymal Modulator (CReMM), a CHD protein expressed by mesenchymal cells. In this study, we analyzed CReMM expression on RNA and protein levels during embryonic development in mouse skeletal tissues. CReMM appears transiently during mesenchymal cell differentiation, being detected first in osteoprogenitors and declining in mature cells. A novel aspect of the study elaborates on in vivo association of CReMM with promoters in cells obtained by laser capture micro-dissection (LCM) technique from periosteum and endochondreal ossification regions. Using chromatin immunoprecipitation (ChIP), we proved that CReMM binds to skeletal tissue-specific promoters: CBFA1, biglycan, osteocalcin (OC), collagen-II, and myosin in a differential manner. The results imply that CReMM selectively interacts with analyzed promoters activated in the tissue at the appropriate time of development. The identification of CReMM and its tissue distribution and function provides an attractive clue for the study of transcriptional regulation of osteogenic cells' maturation.

Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs

Chromatin is a, if not the, hallmark of eukaryotic life. Any molecular process entailing genomic DNA or the nucleus by default provokes or depends on chromatin structural dynamics on various space and time scales. Chromatin dynamics are result of changes in the physico-chemical properties of the chromatin constituents themselves or the nuclear environment. Chromatin has been found in the former case to undergo many different covalent enzyme-mediated chemical modifications. Their identification sheds light on the molecular mechanisms and the physico-chemical properties underlying chromatin dynamics, and allows the development of quantitative models for the chromatin fiber. The abundance of the different modifications, their dynamics, and short- as well as long-range correlation phenomena between different modifications also point to a second layer of genomic coding implemented at the level of chromatin. Especially, gene regulatory coding seems to depend on such a second-level code. The information-theoretical properties of chromatin in the context of gene regulatory coding are discussed. A model for the emergence of cellular differentiation from the intricate interplay between genomic and chromatin code is presented and discussed in light of recent experimental insights.

Oxygen, epigenetics and stem cell fate

Coordinated interactions between the embryo/fetus and its environment are critical for proper development. In addition to acting as metabolic substrates for cellular homeostasis, basic physiological factors, such as oxygen tension, have a profound influence on developmental outcomes. Since the mammalian embryo resides in a physiologically hypoxic environment during gestation, understanding its responses to oxygen deprivation on a cellular level is critical. In this review, we analyze interactions between the hypoxia-inducible factor family of transcriptional regulators and epigenetic mechanisms governing chromatin structure. The ability of hypoxia-inducible factors to interact physically with histone deacetylase (HDAC) enzymes and modulate nuclear HDAC activities places them in the pivotal position of integrating physiological and epigenetic effectors. Multiple embryonic and extra-embryonic stem cell populations in mice and humans rely on this interaction – an important determinant of stem cell fate. Dissection of the pathways involved will provide novel insights into the metabolic as well as molecular determinants of the stem cell niches that allow self-renewal of progenitors in an undifferentiated state.

The human brain and its neural stem cells postmortem: from dead brains to live therapy

Contrary to the traditional dogma of being a relatively invariable and quiescent organ lacking the capability to regenerate, there is now widespread evidence that the human brain harbors multipotent neural stem cells, possibly throughout senescence. These cells can divide and give rise to neuroectodermal progeny in vivo and are now regarded as powerful prospective candidates for repairing or enhancing the functional capability of neural tissue in trauma or diseases associated with degeneration or malperfusion. Hopes primarily rest upon techniques to either recruit endogenous stem cells or to utilize exogenous donor-derived material for transplantation. In the search for suitable human cell sources, embryonic, fetal, and adult stem cells appear highly controversial, as they are accompanied by various still-unresolved moral and legal challenges. Fascinatingly, however, recent reports indicate the successful isolation and expansion of viable neural stem cells from the rodent and human brain within a considerable postmortem interval, suggesting that postmortem neural stem cells could potentially become an acceptable alternative cellular resource. This article will provide a brief overview about neural stem cells, their prominent features, and prospects for a cellular therapy, and will furthermore illuminate the cells in particular with respect to their newly discovered postmortem provenience, their advantage as a potential cell source, and several unfolding forensic considerations. Also, important ethical, social, and legal implications arising from this hitherto unpracticed cellular harvest of brain tissue from the deceased are outlined.

Adult bone marrow stem/progenitor cells (MSCs) are preconditioned by microenvironmental "niches" in culture: a two-stage hypothesis for regulation of MSC fate

Mesenchymal stem cells (MSCs) are clonal, plastic adherent cells from bone marrow that can differentiate into various tissue lineages, including osteoblasts, adipocytes, chondrocytes, myoblasts, hepatocytes, and possibly even neural cells. Because MSCs are multipotent and their numbers are easily expanded in culture, there has been much interest in their clinical potential for tissue repair and gene therapy. Consequently, numerous studies have been carried out demonstrating the migration and multiorgan engraftment potential of MSCs in animal models and in human clinical trials. Understanding the mechanisms behind MSC cell fate determination is not easy, because the molecular processes that drive engraftment and differentiation are complex. Even in an in vitro system, the molecular cues necessary to induce differentiation are not easily identified or reproduced. In this Perspective, we emphasize the importance of microenvironmental factors in culture and suggest that MSC differentiation in vitro is regulated by a two-stage mechanism involving preconditioning by factors in the culture microenvironment followed by response to soluble differentiating factors.