Comparison of neurosphere-like cell clusters derived from dental follicle precursor cells and retinal Müller cells

Proteogenomics for Non-model Ocean-Derived Fungi

Most biological and biomedical experiments are designed and studied using the most common model organisms (MOs) like humans, mice, Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, worms, fruit flies, zebrafish, and Arabidopsis thaliana. These model organisms have been extensively studied and have a well-established set of genetic, physiological, and other tools available for research. In contrast, non-model organisms (NMOs) are those that are not traditionally used in scientific research and do not have a well-established set of genetic or other biological tools available for their study. The majority of MOs are associated with land habitats but rarely with ocean environments. The ocean forms the largest portion of our planet, yet ocean-derived organisms are the least explored, and these organisms are primarily NMOs. However, these are thrilling living entities, such as ocean-derived fungi (ODF). These ODFs are a diverse group of fungi that live in different ocean sectors, including the ocean, estuaries, and coastal ecosystems. These fungi are found to colonize and adapt to different substrates. They are important decomposers in marine ecosystems, breaking down dead organic matter and recycling nutrients. ODFs have adapted to survive in the unique and challenging conditions of the ocean environment, including high salt concentrations, low nutrient availability, and exposure to waves and currents. ODFs are potent producers of natural compounds with pharmaceutical and industrial applications, such as antibiotics, anticancer agents, antivirals, and enzymes for industrial processes. ODFs are an exciting group of fungi; however, these are the least studied because of the nonavailability of MOs from this group. Hence, there is a massive scope of expanding our current knowledge about ODFs, their genetic traits, potential future drug-producing capabilities, and lifestyle traits.With the advent of next-generation DNA sequencing, there is huge potential for the characterization of the genetic material of ODF as NMOs. Parallel proteomic methods also pose huge potential. A marriage of NGS and proteomic methods generates a new avenue called proteogenomics, which focuses on better annotation of existing genomic data. Both methods are getting cheaper and accessible to the research community for studying the proteogenomics of NMOs. Herein, the proteogenomic protocol development and data analyses are illustrated for the ocean-derived fungus Scopulariopsis brevicaulis.

Dental stem cell sphere formation and potential for neural regeneration: A scoping review

Background

Dental stem cells with neurosphere-forming abilities are a promising cell source for the treatment of neural diseases and injuries. This scoping review aimed to systematically map the existing literature on dental sphere formation assays and their characteristics associated with neural regeneration potential.

Methods

The Web of Science, EMBASE, SCOPUS, and PubMed databases were systematically searched for in vitro, animal, and clinical studies and reviews focusing on stem cells isolated from the oral cavity, subsequently cultured as spheres with neural regeneration potential. Data were extracted and evidence was synthesized according to the predetermined variables in the registered protocol.

Results

A total of 35 articles (31 in vitro, 1 combined in vitro and in vivo, and 3 reviews) were included. The predominant method utilized for sphere formation was low-attachment culture. Spheres were characterized using assessment of neural marker expression via confocal microscopy, immunohistochemistry, RT-qPCR, or western blotting. Overall, the synthesized results indicate a lack of in vivo studies investigating the utility of dental neurospheres for neural regeneration, with dental pulp stem cells being the most investigated for their neural regenerative potential.

Conclusion

Dental stem cell spheres demonstrate significant potential for neural regeneration. Several assays and characterizations have been performed to characterized the mechanisms underlying dental sphere formation. Furthermore, in vivo studies are imperative to deduce the neural regenerative potential of stem cells in complex biological environments.

Therapeutic Potential of Oral-Derived Mesenchymal Stem Cells in Retinal Repair

The retina has restricted regeneration ability to recover injured cell layer because of reduced production of neurotrophic factors and increased inhibitory molecules against axon regrowth. A diseased retina could be regenerated by repopulating the damaged tissue with functional cell sources like mesenchymal stem cells (MSCs). The cells are able to release neurotrophic factors (NFs) to boost axonal regeneration and cell maintenance. In the current study, we comprehensively explore the potential of various types of stem cells (SCs) from oral cavity as promising therapeutic options in retinal regeneration. The oral MSCs derived from cranial neural crest cells (CNCCs) which explains their broad neural differentiation potential and secret rich NFs. They are comprised of dental pulp SCs (DPSCs), SCs from exfoliated deciduous teeth (SHED), SCs from apical papilla (SCAP), periodontal ligament-derived SCs (PDLSCs), gingival MSCs (GMSCs), and dental follicle SCs (DFSCs). The Oral MSCs are becoming a promising source of cells for cell-free or cell-based therapeutic approach to recover degenerated retinal. These cells have various mechanisms of action in retinal regeneration including cell replacement and the paracrine effect. It was demonstrated that they have more neuroprotective and neurotrophic effects on retinal cells than immediate replacement of injured cells in retina. This could be the reason that their therapeutic effects would be weakened over time. It can be concluded that neuronal and retinal regeneration through these cells is most likely due to their NFs that dramatically suppress oxidative stress, inflammation, and apoptosis. Although, oral MSCs are attractive therapeutic options for retinal injuries, more preclinical and clinical investigations are required.

Preliminary analysis of proteome alterations in non-aneurysmal, internal mammary artery tissue from patients with abdominal aortic aneurysms

Objective

The pathogenesis of abdominal aortic aneurysms (AAA) involves a disturbed balance of breakdown and buildup of arterial proteins. We envision that individuals with AAA carry generalized arterial protein alterations either because of effects of genetically or environmental AAA risk factors or because of compensatory changes due to signaling molecules released from the affected aneurysmal tissue.

Approach

Protein extraction and quantitative proteome analysis by LC-MS/MS (liquid chromatography-mass spectrometry) was done on individual samples from the internal mammary artery from 11 individuals with AAA and 33 sex- and age-matched controls without AAA. Samples were selected from a biobank of leftover internal mammary arterial tissue gathered at coronary by-pass operations.

Results

We identified and quantitated 877 proteins, of which 44 were differentially expressed between the two groups (nominal p-values without correction for multiple testing). Some proteins related to the extracellular matrix displayed altered concentrations in the AAA group, particularly among elastin-related molecules [elastin, microfibrillar-associated protein 4 (MFAP4), lysyl oxidase]. In addition, several histones e.g. (e.g. HIST1H1E, HIST1H2BB) and other vascular cell proteins (e.g. versican, type VI collagen) were altered.

Conclusions

Our results support the notion that generalized alterations occur in the arterial tree in patients with AAA. Elastin-related proteins and histones seem to be part of such changes, however these preliminary results require replication in an independent set of specimens and validation by functional studies.

Quantitative Proteome Analysis Reveals Increased Content of Basement Membrane Proteins in Arteries From Patients With Type 2 Diabetes Mellitus and Lower Levels Among Metformin Users

BACKGROUND

The increased risk of cardiovascular diseases in type 2 diabetes mellitus has been extensively documented, but the origins of the association remain largely unknown. We sought to determine changes in protein expressions in arterial tissue from patients with type 2 diabetes mellitus and moreover hypothesized that metformin intake influences the protein composition.

METHODS AND RESULTS

We analyzed nonatherosclerotic repair arteries gathered at coronary bypass operations from 30 patients with type 2 diabetes mellitus and from 30 age- and sex-matched nondiabetic individuals. Quantitative proteome analysis was performed by isobaric tag for relative and absolute quantitation-labeling and liquid chromatography-mass spectrometry, tandem mass spectrometry analysis on individual arterial samples. The amounts of the basement membrane components, α1-type IV collagen and α2-type IV collagen, γ1-laminin and β2-laminin, were significantly increased in patients with diabetes mellitus. Moreover, the expressions of basement membrane components and other vascular proteins were significantly lower among metformin users when compared with nonusers. Patients treated with or without metformin had similar levels of hemoglobin A1c, cholesterol, and blood pressure. In addition, quantitative histomorphometry showed increased area fractions of collagen-stainable material in tunica intima and media among patients with diabetes mellitus.

CONCLUSIONS

The distinct accumulation of arterial basement membrane proteins in type 2 diabetes mellitus discloses a similarity between the diabetic macroangiopathy and microangiopathy and suggests a molecular explanation behind the alterations in vascular remodeling, biomechanical properties, and aneurysm formation described in diabetes mellitus. The lower amounts of basement membrane components in metformin-treated individuals are compatible with the hypothesis of direct beneficial drug effects on the matrix composition in the vasculature.

Evaluation of implant-materials as cell carriers for dental stem cells under in vitro conditions

BACKGROUND

Dental stem cells in combination with implant materials may become an alternative to autologous bone transplants. For tissue engineering different types of soft and rigid implant materials are available, but little is known about the viability and the osteogenic differentiation of dental stem cells on these different types of materials. According to previous studies we proposed that rigid bone substitute materials are superior to soft materials for dental tissue engineering.

METHODS

We evaluated the proliferation, the induction of apoptosis and the osteogenic differentiation of dental stem/progenitor cells on a synthetic bone-like material and on an allograft product. The soft materials silicone and polyacrylamide (PA) were used for comparison. Precursor cells from the dental follicle (DFCs) and progenitor cells from the dental apical papilla of retained third molar tooth (dNC-PCs) were applied as dental stem cells in our study.

RESULTS

Both dental cell types attached and grew on rigid bone substitute materials, but they did not grow on soft materials. Moreover, rigid bone substitute materials only sustained the osteogenic differentiation of dental stem cells, although the allograft product induced apoptosis in both dental cell types. Remarkably, PA, silicone and the synthetic bone substitute material did not induce the apoptosis in dental cells.

CONCLUSIONS

Our work supports the hypothesis that bone substitute materials are suitable for dental stem cell tissue engineering. Furthermore, we also suggest that the induction of apoptosis by bone substitute materials may not impair the proliferation and the differentiation of dental stem cells.

A site-specific phosphorylation of the focal adhesion kinase controls the formation of spheroid cell clusters

Human dental follicle cells (DFCs) are ectomesenchymal multipotent stem cells that form spheroid cell clusters (SCCs) under serum free medium cell culture conditions (SFM). Until today, molecular mechanisms for the formation of SCCs are unknown. In this study a quantitative phosphoproteomics approach revealed regulated phosphorylated proteins in SCCs, which were derived from DFCs after 24 and 48 h in SFM. These regulated proteins were categorized using the Kyoto encyclopedia of genes and genomes program. Here, cellular processes and signaling pathway were identified such as the focal adhesion kinase (FAK) signaling pathway. In addition to the phosphoproteomics approach we showed that a specific phosphorylation of FAK (Y397) was required for the formation of SCCs. In conclusion, this study disclosed the phosphoproteome of SCCs for the first time and showed that the FAK signaling pathway is required for the formation of SCCs.

Cell shape and cardiosphere differentiation: a revelation by proteomic profiling

Stem cells (embryonic stem cells, somatic stem cells such as neural stem cells, and cardiac stem cells) and cancer cells are known to aggregate and form spheroid structures. This behavior is common in undifferentiated cells and may be necessary for adapting to certain conditions such as low-oxygen levels or to maintain undifferentiated status in microenvironments including stem cell niches. In order to decipher the meaning of this spheroid structure, we established a cardiosphere clone (CSC-21E) derived from the rat heart which can switch its morphology between spheroid and nonspheroid. Two forms, floating cardiospheres and dish-attached flat cells, could be switched reversibly by changing the cell culture condition. We performed differential proteome analysis studies and obtained protein profiles distinct between spherical forms and flat cells. From protein profiling analysis, we found upregulation of glycolytic enzymes in spheroids with some stress proteins switched in expression levels between these two forms. Evidence has been accumulating that certain chaperone/stress proteins are upregulated in concert with cellular changes including proliferation and differentiation. We would like to discuss the possible mechanism of how these aggregates affect cell differentiation and/or other cellular functions.

α3Na+/K+-ATPase deficiency causes brain ventricle dilation and abrupt embryonic motility in zebrafish

Na(+)/K(+)-ATPases are transmembrane ion pumps that maintain ion gradients across the basolateral plasma membrane in all animal cells to facilitate essential biological functions. Mutations in the Na(+)/K(+)-ATPase α3 subunit gene (ATP1A3) cause rapid-onset dystonia-parkinsonism, a rare movement disorder characterized by sudden onset of dystonic spasms and slow movements. In the brain, ATP1A3 is principally expressed in neurons. In zebrafish, the transcripts of the two ATP1A3 orthologs, Atp1a3a and Atp1a3b, show distinct expression in the brain. Surprisingly, targeted knockdown of either Atp1a3a or Atp1a3b leads to brain ventricle dilation, a likely consequence of ion imbalances across the plasma membrane that cause accumulation of cerebrospinal fluid in the ventricle. The brain ventricle dilation is accompanied by a depolarization of spinal Rohon-Beard neurons in Atp1a3a knockdown embryos, suggesting impaired neuronal excitability. This is further supported by Atp1a3a or Atp1a3b knockdown results where altered responses to tactile stimuli as well as abnormal motility were observed. Finally, proteomic analysis identified several protein candidates highlighting proteome changes associated with the knockdown of Atp1a3a or Atp1a3b. Our data thus strongly support the role of α3Na(+)/K(+)-ATPase in zebrafish motility and brain development, associating for the first time the α3Na(+)/K(+)-ATPase deficiency with brain ventricle dilation.

The α2Na+/K+-ATPase is critical for skeletal and heart muscle function in zebrafish

The Na+/K+-ATPase generates ion gradients across the plasma membrane, essential for multiple cellular functions. In mammals, four different Na+/K+-ATPase α-subunit isoforms are associated with characteristic cell-type expression profiles and kinetics. We found the zebrafish α2Na+/K+-ATPase associated with striated muscles and that α2Na+/K+-ATPase knockdown causes a significant depolarization of the resting membrane potential in slow-twitch fibers of skeletal muscles. Abrupt mechanosensory responses were observed in α2Na+/K+-ATPase deficient embryos, possibly linked to a postsynaptic defect. The α2Na+/K+-ATPase deficiency reduced the heart rate and caused a loss of left-right asymmetry in the heart tube. Similar phenotypes observed by knockdown of the Na+/Ca2+ exchanger indicated a role for the interplay between these two proteins on the observed phenotypes. Furthermore, proteomics identified up- and down-regulation of specific phenotype-related proteins, such as parvalbumin, CaM, GFAP and multiple kinases, thus highlighting a potential proteome change associated with the dynamics of α2Na+/K+-ATPase. Taken together, our findings display that zebrafish α2Na+/K+-ATPase is important for skeletal and heart muscle functions.

Proteomics approaches in the identification of molecular signatures of mesenchymal stem cells

Mesenchymal stem cells (MSCs) are undifferentiated, multi-potent stem cells with the ability to renew. They can differentiate into many types of terminal cells, such as osteoblasts, chondrocytes, adipocytes, myocytes, and neurons. These cells have been applied in tissue engineering as the main cell type to regenerate new tissues. However, a number of issues remain concerning the use of MSCs, such as cell surface markers, the determining factors responsible for their differentiation to terminal cells, and the mechanisms whereby growth factors stimulate MSCs. In this chapter, we will discuss how proteomic techniques have contributed to our current knowledge and how they can be used to address issues currently facing MSC research. The application of proteomics has led to the identification of a special pattern of cell surface protein expression of MSCs. The technique has also contributed to the study of a regulatory network of MSC differentiation to terminal differentiated cells, including osteocytes, chondrocytes, adipocytes, neurons, cardiomyocytes, hepatocytes, and pancreatic islet cells. It has also helped elucidate mechanisms for growth factor-stimulated differentiation of MSCs. Proteomics can, however, not reveal the accurate role of a special pathway and must therefore be combined with other approaches for this purpose. A new generation of proteomic techniques have recently been developed, which will enable a more comprehensive study of MSCs.