High-throughput approaches for the analysis of extrinsic regulators of stem cell fate

Towards organoid culture without Matrigel

Organoids-cellular aggregates derived from stem or progenitor cells that recapitulate organ function in miniature-are of growing interest in developmental biology and medicine. Organoids have been developed for organs and tissues such as the liver, gut, brain, and pancreas; they are used as organ surrogates to study a wide range of questions in basic and developmental biology, genetic disorders, and therapies. However, many organoids reported to date have been cultured in Matrigel, which is prepared from the secretion of Engelbreth-Holm-Swarm mouse sarcoma cells; Matrigel is complex and poorly defined. This complexity makes it difficult to elucidate Matrigel-specific factors governing organoid development. In this review, we discuss promising Matrigel-free methods for the generation and maintenance of organoids that use decellularized extracellular matrix (ECM), synthetic hydrogels, or gel-forming recombinant proteins.

High-Throughput Routes to Biomaterials Discovery

Many existing clinical treatments are limited in their ability to completely restore decreased or lost tissue and organ function, an unenviable situation only further exacerbated by a globally aging population. As a result, the demand for new medical interventions has increased substantially over the past 20 years, with the burgeoning fields of gene therapy, tissue engineering, and regenerative medicine showing promise to offer solutions for full repair or replacement of damaged or aging tissues. Success in these fields, however, inherently relies on biomaterials that are engendered with the ability to provide the necessary biological cues mimicking native extracellular matrixes that support cell fate. Accelerating the development of such "directive" biomaterials requires a shift in current design practices toward those that enable rapid synthesis and characterization of polymeric materials and the coupling of these processes with techniques that enable similarly rapid quantification and optimization of the interactions between these new material systems and target cells and tissues. This manuscript reviews recent advances in combinatorial and high-throughput (HT) technologies applied to polymeric biomaterial synthesis, fabrication, and chemical, physical, and biological screening with targeted end-point applications in the fields of gene therapy, tissue engineering, and regenerative medicine. Limitations of, and future opportunities for, the further application of these research tools and methodologies are also discussed.

High-throughput 3D screening for differentiation of hPSC-derived cell therapy candidates

The emergence of several cell therapy candidates in the clinic is an encouraging sign for human diseases/disorders that currently have no effective treatment; however, scalable production of these cell therapies has become a bottleneck. To overcome this barrier, three-dimensional (3D) cell culture strategies have been considered for enhanced cell production. Here, we demonstrate a high-throughput 3D culture platform used to systematically screen 1200 culture conditions with varying doses, durations, dynamics, and combinations of signaling cues to derive oligodendrocyte progenitor cells and midbrain dopaminergic neurons from human pluripotent stem cells (hPSCs). Statistical models of the robust dataset reveal previously unidentified patterns about cell competence to Wnt, retinoic acid, and sonic hedgehog signals, and their interactions, which may offer insights into the combinatorial roles these signals play in human central nervous system development. These insights can be harnessed to optimize production of hPSC-derived cell replacement therapies for a range of neurological indications.

An Update on the Use of Alginate in Additive Biofabrication Techniques

BACKGROUND

Solid free forming (SFF) technique also called additive manufacturing process is immensely popular for biofabrication owing to its high accuracy, precision and reproducibility.

METHOD

SFF techniques like stereolithography, selective laser sintering, fused deposition modeling, extrusion printing, and inkjet printing create three dimension (3D) structures by layer by layer processing of the material. To achieve desirable results, selection of the appropriate technique is an important aspect and it is based on the nature of biomaterial or bioink to be processed.

RESULT & CONCLUSION

Alginate is a commonly employed bioink in biofabrication process, attributable to its nontoxic, biodegradable and biocompatible nature; low cost; and tendency to form hydrogel under mild conditions. Furthermore, control on its rheological properties like viscosity and shear thinning, makes this natural anionic polymer an appropriate candidate for many of the SFF techniques. It is endeavoured in the present review to highlight the status of alginate as bioink in various SFF techniques.

High-throughput stem cell-based phenotypic screening through microniches

Methods for screening combinations of signals for their effects on stem cell behavior are needed in the field of tissue engineering. We introduce a microgel-based screening platform for testing combinations of proteins on stem cell fate.

Artificial niche microarrays for identifying extrinsic cell-fate determinants

The complex cellular microenvironment plays an important role in determining cell fate. For example, stem cells located in a microenvironment termed niche integrate a wide variety of extrinsic cues to take distinct fate choices. Capturing this multiple-input/multiple-output system in vitro has proven to be very challenging. In order to address this issue, we developed and validated a microfabricated cellular array platform, termed artificial niche microarrays, which is capable of performing high-throughput single-cell assays under physiologically relevant conditions. The platform allows exposing cultured cells to differential signaling cues displayed on soft hydrogel substrates having variable stiffness. The behavior of the seeded cells can be readily quantified across over 2000 multivariate microenvironments. Here we describe a pipeline for performing multifactorial, image-based assays with these artificial niche microarrays. The procedure details the steps from microarray production, cell culture, cell phenotyping, data extraction to statistical analysis.

Visualizing Intrapopulation Hematopoietic Cell Heterogeneity with Self-Organizing Maps of SIMS Data

Characterization of the heterogeneity within stem cell populations, which affects their differentiation potential, is necessary for the design of artificial cultures for stem cell expansion. In this study, we assessed whether self-organizing maps (SOMs) of single-cell time-of-flight secondary ion mass spectrometry (TOF-SIMS) data provide insight into the spectral, and thus the related functional heterogeneity between and within three hematopoietic cell populations. SOMs were created of TOF-SIMS data from individual hematopoietic stem and progenitor cells (HSPCs), lineage-committed common lymphoid progenitors (CLPs), and fully differentiated B cells that had been isolated from murine bone marrow via conventional flow cytometry. The positions of these cells on the SOMs and the spectral variation between adjacent map units, shown on the corresponding unified distance matrix (U-matrix), indicated the CLPs exhibited the highest intrapopulation spectral variation, regardless of the age of the donor mice. SOMs of HSPCs, CLPs, and B cells isolated from young and old mice using the same surface antigen profiles revealed the HSPCs exhibited the most age-related spectral variation, whereas B cells exhibited the least. These results demonstrate that SOMs of single-cell spectra enable characterizing the heterogeneity between and within cell populations that lie along distinct differentiation pathways.

Controlling Differentiation of Stem Cells for Developing Personalized Organ-on-Chip Platforms

Organ-on-chip (OOC) platforms have attracted attentions of pharmaceutical companies as powerful tools for screening of existing drugs and development of new drug candidates. OOCs have primarily used human cell lines or primary cells to develop biomimetic tissue models. However, the ability of human stem cells in unlimited self-renewal and differentiation into multiple lineages has made them attractive for OOCs. The microfluidic technology has enabled precise control of stem cell differentiation using soluble factors, biophysical cues, and electromagnetic signals. This study discusses different tissue- and organ-on-chip platforms (i.e., skin, brain, blood-brain barrier, bone marrow, heart, liver, lung, tumor, and vascular), with an emphasis on the critical role of stem cells in the synthesis of complex tissues. This study further recaps the design, fabrication, high-throughput performance, and improved functionality of stem-cell-based OOCs, technical challenges, obstacles against implementing their potential applications, and future perspectives related to different experimental platforms.

Novel biomaterials to study neural stem cell mechanobiology and improve cell-replacement therapies

Neural stem cells (NSCs) are a valuable cell source for tissue engineering, regenerative medicine, disease modeling, and drug screening applications. Analogous to other stem cells, NSCs are tightly regulated by their microenvironmental niche, and prior work utilizing NSCs as a model system with engineered biomaterials has offered valuable insights into how biophysical inputs can regulate stem cell proliferation, differentiation, and maturation. In this review, we highlight recent exciting studies with innovative material platforms that enable narrow stiffness gradients, mechanical stretching, temporal stiffness switching, and three-dimensional culture to study NSCs. These studies have significantly advanced our knowledge of how stem cells respond to an array of different biophysical inputs and the underlying mechanosensitive mechanisms. In addition, we discuss efforts to utilize engineered material scaffolds to improve NSC-based translational efforts and the importance of mechanobiology in tissue engineering applications.

Functional and Biomimetic Materials for Engineering of the Three-Dimensional Cell Microenvironment

The cell microenvironment has emerged as a key determinant of cell behavior and function in development, physiology, and pathophysiology. The extracellular matrix (ECM) within the cell microenvironment serves not only as a structural foundation for cells but also as a source of three-dimensional (3D) biochemical and biophysical cues that trigger and regulate cell behaviors. Increasing evidence suggests that the 3D character of the microenvironment is required for development of many critical cell responses observed in vivo, fueling a surge in the development of functional and biomimetic materials for engineering the 3D cell microenvironment. Progress in the design of such materials has improved control of cell behaviors in 3D and advanced the fields of tissue regeneration, in vitro tissue models, large-scale cell differentiation, immunotherapy, and gene therapy. However, the field is still in its infancy, and discoveries about the nature of cell-microenvironment interactions continue to overturn much early progress in the field. Key challenges continue to be dissecting the roles of chemistry, structure, mechanics, and electrophysiology in the cell microenvironment, and understanding and harnessing the roles of periodicity and drift in these factors. This review encapsulates where recent advances appear to leave the ever-shifting state of the art, and it highlights areas in which substantial potential and uncertainty remain.

Cellular self-assembly and biomaterials-based organoid models of development and diseases

Organogenesis and morphogenesis have informed our understanding of physiology, pathophysiology, and avenues to create new curative and regenerative therapies. Thus far, this understanding has been hindered by the lack of a physiologically relevant yet accessible model that affords biological control. Recently, three-dimensional ex vivo cellular cultures created through cellular self-assembly under natural extracellular matrix cues or through biomaterial-based directed assembly have been shown to physically resemble and recapture some functionality of target organs. These "organoids" have garnered momentum for their applications in modeling human development and disease, drug screening, and future therapy design or even organ replacement. This review first discusses the self-organizing organoids as materials with emergent properties and their advantages and limitations. We subsequently describe biomaterials-based strategies used to afford more control of the organoid's microenvironment and ensuing cellular composition and organization. In this review, we also offer our perspective on how multifunctional biomaterials with precise spatial and temporal control could ultimately bridge the gap between in vitro organoid platforms and their in vivo counterparts.

STATEMENT OF SIGNIFICANCE

Several notable reviews have highlighted PSC-derived organoids and 3D aggregates, including embryoid bodies, from a development and cellular assembly perspective. The focus of this review is to highlight the materials-based approaches that cells, including PSCs and others, adopt for self-assembly and the controlled development of complex tissues, such as that of the brain, gut, and immune system.

A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces

Microfabricated cellular microarrays, which consist of contact-printed combinations of biomolecules on an elastic hydrogel surface, provide a tightly controlled, high-throughput engineered system for measuring the impact of arrayed biochemical signals on cell differentiation. Recent efforts using cell microarrays have demonstrated their utility for combinatorial studies in which many microenvironmental factors are presented in parallel. However, these efforts have focused primarily on investigating the effects of biochemical cues on cell responses. Here, we present a cell microarray platform with tunable material properties for evaluating both cell differentiation by immunofluorescence and biomechanical cell-substrate interactions by traction force microscopy. To do so, we have developed two different formats utilizing polyacrylamide hydrogels of varying Young's modulus fabricated on either microscope slides or glass-bottom Petri dishes. We provide best practices and troubleshooting for the fabrication of microarrays on these hydrogel substrates, the subsequent cell culture on microarrays, and the acquisition of data. This platform is well-suited for use in investigations of biological processes for which both biochemical (e.g., extracellular matrix composition) and biophysical (e.g., substrate stiffness) cues may play significant, intersecting roles.

Cardiac Mechanoperception: A Life-Long Story from Early Beats to Aging and Failure

The life-long story of the heart starts concomitantly with primary differentiation events occurring in multipotent progenitors located in the so-called heart tube. This initially tubular structure starts a looping process, which leads to formation of the final four-chambered heart with a primary contribution of geometric and position-associated cell sensing. While this establishes the correct patterning of the final cardiac structure, it also provides feedbacks to fundamental cellular machineries controlling proliferation and differentiation, thus ensuring a coordinated restriction of cell growth and a myocyte terminal differentiation. Novel evidences provided by embryological and cell engineering studies have clarified the relevance of mechanics-supported position sensing for the correct recognition of cell fate inside developing embryos and multicellular aggregates. One of the main components of this pathway, the Hippo-dependent signal transduction machinery, is responsible for cell mechanics intracellular transduction with important consequences for gene transcription and cell growth control. Being the Hippo pathway also directly connected to stress responses and altered metabolism, it is tempting to speculate that permanent alterations of mechanosensing may account for modifying self-renewal control in tissue homeostasis. In the present contribution, we translate these concepts to the aging process and the failing of the human heart, two pathophysiologic conditions that are strongly affected by stress responses and altered metabolism.

Glycosaminoglycan-Based Biohybrid Hydrogels: A Sweet and Smart Choice for Multifunctional Biomaterials

Glycosaminoglycans (GAGs) govern important functional characteristics of the extracellular matrix (ECM) in living tissues. Incorporation of GAGs into biomaterials opens up new routes for the presentation of signaling molecules, providing control over development, homeostasis, inflammation, and tumor formation and progression. Recent approaches to GAG-based materials are reviewed, highlighting the formation of modular, tunable biohybrid hydrogels by covalent and non-covalent conjugation schemes, including both theory-driven design concepts and advanced processing technologies. Examples of the application of the resulting materials in biomedical studies are provided. For perspective, solid-phase and chemoenzymatic oligosaccharide synthesis methods for GAG-derived motifs, rational and high-throughput design strategies for GAG-based materials, and the utilization of the factor-scavenging characteristics of GAGs are highlighted.

Integrating Concepts of Material Mechanics, Ligand Chemistry, Dimensionality and Degradation to Control Differentiation of Mesenchymal Stem Cells

The role of substrate mechanics in guiding mesenchymal stem cell (MSC) fate has been the focus of much research over the last decade. More recently, the complex interplay between substrate mechanics and other material properties such as ligand chemistry and substrate degradability to regulate MSC differentiation has begun to be elucidated. Additionally, there are several changes in the presentation of these material properties as the dimensionality is altered from two- to three-dimensional substrates, which may fundamentally alter our understanding of substrate-induced mechanotransduction processes. In this review, an overview of recent findings that highlight the material properties that are important in guiding MSC fate decisions is presented, with a focus on underlining gaps in our existing knowledge and proposing potential directions for future research.

Regeneration of the lung: Lung stem cells and the development of lung mimicking devices

Inspired by the increasing burden of lung associated diseases in society and an growing demand to accommodate patients, great efforts by the scientific community produce an increasing stream of data that are focused on delineating the basic principles of lung development and growth, as well as understanding the biomechanical properties to build artificial lung devices. In addition, the continuing efforts to better define the disease origin, progression and pathology by basic scientists and clinicians contributes to insights in the basic principles of lung biology. However, the use of different model systems, experimental approaches and readout systems may generate somewhat conflicting or contradictory results. In an effort to summarize the latest developments in the lung epithelial stem cell biology, we provide an overview of the current status of the field. We first describe the different stem cells, or progenitor cells, residing in the homeostatic lung. Next, we focus on the plasticity of the different cell types upon several injury-induced activation or repair models, and highlight the regenerative capacity of lung cells. Lastly, we summarize the generation of lung mimics, such as air-liquid interface cultures, organoids and lung on a chip, that are required to test emerging hypotheses. Moreover, the increasing collaboration between distinct specializations will contribute to the eventual development of an artificial lung device capable of assisting reduced lung function and capacity in human patients.

Polymer microarray technology for stem cell engineering

Stem cells hold remarkable promise for applications in tissue engineering and disease modeling. During the past decade, significant progress has been made in developing soluble factors (e.g., small molecules and growth factors) to direct stem cells into a desired phenotype. However, the current lack of suitable synthetic materials to regulate stem cell activity has limited the realization of the enormous potential of stem cells. This can be attributed to a large number of materials properties (e.g., chemical structures and physical properties of materials) that can affect stem cell fate. This makes it challenging to design biomaterials to direct stem cell behavior. To address this, polymer microarray technology has been developed to rapidly identify materials for a variety of stem cell applications. In this article, we summarize recent developments in polymer array technology and their applications in stem cell engineering.

STATEMENT OF SIGNIFICANCE

Stem cells hold remarkable promise for applications in tissue engineering and disease modeling. In the last decade, significant progress has been made in developing chemically defined media to direct stem cells into a desired phenotype. However, the current lack of the suitable synthetic materials to regulate stem cell activities has been limiting the realization of the potential of stem cells. This can be attributed to the number of variables in material properties (e.g., chemical structures and physical properties) that can affect stem cells. Polymer microarray technology has shown to be a powerful tool to rapidly identify materials for a variety of stem cell applications. Here we summarize recent developments in polymer array technology and their applications in stem cell engineering.

Hydrogel arrays formed via differential wettability patterning enable combinatorial screening of stem cell behavior

Here, we have developed a novel method for forming hydrogel arrays using surfaces patterned with differential wettability. Our method for benchtop array formation is suitable for enhanced-throughput, combinatorial screening of biochemical and biophysical cues from chemically defined cell culture substrates. We demonstrated the ability to generate these arrays without the need for liquid handling systems and screened the combinatorial effects of substrate stiffness and immobilized cell adhesion peptide concentration on human mesenchymal stem cell (hMSC) behavior during short-term 2-dimensional cell culture. Regardless of substrate stiffness, hMSC initial cell attachment, spreading, and proliferation were linearly correlated with immobilized CRGDS peptide concentration. Increasing substrate stiffness also resulted in increased hMSC initial cell attachment, spreading, and proliferation; however, examination of the combinatorial effects of CRGDS peptide concentration and substrate stiffness revealed potential interplay between these distinct substrate signals. Maximal hMSC proliferation seen on substrates with either high stiffness or high CRGDS peptide concentration suggests that some baseline level of cytoskeletal tension was required for hMSC proliferation on hydrogel substrates and that multiple substrate signals could be engineered to work in synergy to promote mechanosensing and regulate cell behavior.

STATEMENT OF SIGNIFICANCE

Our novel array formation method using surfaces patterned with differential wettability offers the advantages of benchtop array formation for 2-dimensional cell cultures and enhanced-throughput screening without the need for liquid handling systems. Hydrogel arrays formed via our method are suitable for screening the influence of chemical (e.g. cell adhesive ligands) and physical (stiffness, size, shape, and thickness) substrate properties on stem cell behavior. The arrays are also fully compatible with commercially available micro-array add-on systems, which allows for simultaneous control of the insoluble and soluble cell culture environment. This study used hydrogel arrays to demonstrate that synergy between cell adhesion and mechanosensing can be used to regulate hMSC behavior.

Combinatorial Biomolecular Nanopatterning for High-Throughput Screening of Stem-Cell Behavior

A novel combinatorial biomolecular nanopatterning method is reported, in which multiple biomolecular ligands can be patterned in multiple nanoscale dimensions on a single surface. The applicability of the combinatorial platform toward cell-biology applications is demonstrated by screening the adhesion behavior of a population of human dental pulp stem cell (hDPSC) on 64 combinations of nanopatterned extracellular matrix (ECM) proteins in parallel.

The design of reversible hydrogels to capture extracellular matrix dynamics

The extracellular matrix (ECM) is a dynamic environment that constantly provides physical and chemical cues to embedded cells. Much progress has been made in engineering hydrogels that can mimic the ECM, but hydrogel properties are, in general, static. To recapitulate the dynamic nature of the ECM, many reversible chemistries have been incorporated into hydrogels to regulate cell spreading, biochemical ligand presentation and matrix mechanics. For example, emerging trends include the use of molecular photoswitches or biomolecule hybridization to control polymer chain conformation, thereby enabling the modulation of the hydrogel between two states on demand. In addition, many non-covalent, dynamic chemical bonds have found increasing use as hydrogel crosslinkers or tethers for cell signalling molecules. These reversible chemistries will provide greater temporal control of adhered cell behaviour, and they allow for more advanced in vitro models and tissue-engineering scaffolds to direct cell fate.

Identifying States along the Hematopoietic Stem Cell Differentiation Hierarchy with Single Cell Specificity via Raman Spectroscopy

A major challenge for expanding specific types of hematopoietic cells ex vivo for the treatment of blood cell pathologies is identifying the combinations of cellular and matrix cues that direct hematopoietic stem cells (HSC) to self-renew or differentiate into cell populations ex vivo. Microscale screening platforms enable minimizing the number of rare HSCs required to screen the effects of numerous cues on HSC fate decisions. These platforms create a strong demand for label-free methods that accurately identify the fate decisions of individual hematopoietic cells at specific locations on the platform. We demonstrate the capacity to identify discrete cells along the HSC differentiation hierarchy via multivariate analysis of Raman spectra. Notably, cell state identification is accurate for individual cells and independent of the biophysical properties of the functionalized polyacrylamide gels upon which these cells are cultured. We report partial least-squares discriminant analysis (PLS-DA) models of single cell Raman spectra enable identifying four dissimilar hematopoietic cell populations across the HSC lineage specification. Successful discrimination was obtained for a population enriched for long-term repopulating HSCs (LT-HSCs) versus their more differentiated progeny, including closely related short-term repopulating HSCs (ST-HSCs) and fully differentiated lymphoid (B cells) and myeloid (granulocytes) cells. The lineage-specific differentiation states of cells from these four subpopulations were accurately identified independent of the stiffness of the underlying biomaterial substrate, indicating subtle spectral variations that discriminated these populations were not masked by features from the culture substrate. This approach enables identifying the lineage-specific differentiation stages of hematopoietic cells on biomaterial substrates of differing composition and may facilitate correlating hematopoietic cell fate decisions with the extrinsic cues that elicited them.

A synthetic hydrogel for the high-throughput study of cell-ECM interactions

It remains extremely challenging to dissect the cooperative influence of multiple extracellular matrix (ECM) parameters on cell behaviour. This stems in part from a lack of easily deployable strategies for the combinatorial variation of matrix biochemical and biophysical properties. Here we describe a simple, high-throughput platform based on light-modulated hyaluronic acid hydrogels that enables imposition of mutually independent and spatially continuous gradients of ligand density and substrate stiffness. We validate this system by showing that it can support mechanosensitive differentiation of mesenchymal stem cells. We also use it to show that the oncogenic microRNA, miR18a, is nonlinearly regulated by matrix stiffness and fibronectin density in glioma cells. The parallelization of experiments enabled by this platform allows condensation of studies that would normally require hundreds of independent hydrogels to a single substrate. This system is a highly accessible, high-throughput technique to study the combinatorial variation of biophysical and biochemical signals in a single experimental paradigm.

Multiple extracellular matrix parameters influence cellular behaviour, but it is difficult to dissect their cooperative contributions. Here the authors describe a hydrogel system in which ligand density and substrate stiffness can be tuned orthogonally to study the contribution of combinations of these parameters simultaneously.

Three-dimensional, soft neotissue arrays as high throughput platforms for the interrogation of engineered tissue environments

Local signals from tissue-specific extracellular matrix (ECM) microenvironments, including matrix adhesive ligand, mechanical elasticity and micro-scale geometry, are known to instruct a variety of stem cell differentiation processes. Likewise, these signals converge to provide multifaceted, mechanochemical cues for highly-specific tissue morphogenesis or regeneration. Despite accumulated knowledge about the individual and combined roles of various mechanochemical ECM signals in stem cell activities on 2-dimensional matrices, the understandings of morphogenetic or regenerative 3-dimenstional tissue microenvironments remain very limited. To that end, we established high-throughput platforms based on soft, fibrous matrices with various combinatorial ECM proteins meanwhile highly-tunable in elasticity and 3-dimensional geometry. To demonstrate the utility of our platform, we evaluated 64 unique combinations of 6 ECM proteins (collagen I, collagen III, collagen IV, laminin, fibronectin, and elastin) on the adhesion, spreading and fate commitment of mesenchymal stem cell (MSCs) under two substrate stiffness (4.6 kPa, 20 kPa). Using this technique, we identified several neotissue microenvironments supporting MSC adhesion, spreading and differentiation toward early vascular lineages. Manipulation of the matrix properties, such as elasticity and geometry, in concert with ECM proteins will permit the investigation of multiple and distinct MSC environments. This paper demonstrates the practical application of high through-put technology to facilitate the screening of a variety of engineered microenvironments with the aim to instruct stem cell differentiation.

Identifying the lineages of individual cells in cocultures by multivariate analysis of Raman spectra

The cellular and matrix cues that induce stem cell differentiation into distinct cell lineages must be identified to permit the ex vivo expansion of desired cell populations for clinical applications. Combinatorial biomaterials enable screening multiple different microenvironments while using small numbers of rare stem cells. New methods to identify the phenotypes of individual cells in cocultures with location specificity would increase the efficiency and throughput of these screening platforms. Here, we demonstrate that partial least-squares discriminant analysis (PLS-DA) models of calibration Raman spectra from cells in pure cultures can be used to identify the lineages of individual cells in more complex culture environments. The calibration Raman spectra were collected from individual cells of four different lineages, and a PLS-DA model that captured the Raman spectral profiles characteristic of each cell line was created. The application of these models to Raman spectra from test sets of cells indicated individual, fixed and living cells in separate monocultures, as well as those in more complex culture environments, such as cocultures, could be identified with low error. Cells from populations with very similar biochemistries could also be identified with high accuracy. We show that these identifications are based on reproducible cell-related spectral features, and not spectral contributions from the culture environment. This work demonstrates that PLS-DA of Raman spectra acquired from pure monocultures provides an objective, noninvasive, and label-free approach for accurately identifying the lineages of individual, living cells in more complex coculture environments.

Development and integration of block operations for data invariant automation of digital preprocessing and analysis of biological and biomedical Raman spectra

High-throughput information extraction from large numbers of Raman spectra is becoming an increasingly taxing problem due to the proliferation of new applications enabled using advances in instrumentation. Fortunately, in many of these applications, the entire process can be automated, yielding reproducibly good results with significant time and cost savings. Information extraction consists of two stages, preprocessing and analysis. We focus here on the preprocessing stage, which typically involves several steps, such as calibration, background subtraction, baseline flattening, artifact removal, smoothing, and so on, before the resulting spectra can be further analyzed. Because the results of some of these steps can affect the performance of subsequent ones, attention must be given to the sequencing of steps, the compatibility of these sequences, and the propensity of each step to generate spectral distortions. We outline here important considerations to effect full automation of Raman spectral preprocessing: what is considered full automation; putative general principles to effect full automation; the proper sequencing of processing and analysis steps; conflicts and circularities arising from sequencing; and the need for, and approaches to, preprocessing quality control. These considerations are discussed and illustrated with biological and biomedical examples reflecting both successful and faulty preprocessing.

Light-triggered in vivo activation of adhesive peptides regulates cell adhesion, inflammation and vascularization of biomaterials

Materials engineered to elicit targeted cellular responses in regenerative medicine must display bioligands with precise spatial and temporal control. Although materials with temporally regulated presentation of bioadhesive ligands using external triggers, such as light and electric fields, have recently been realized for cells in culture, the impact of in vivo temporal ligand presentation on cell-material responses is unknown. Here, we present a general strategy to temporally and spatially control the in vivo presentation of bioligands using cell-adhesive peptides with a protecting group that can be easily removed via transdermal light exposure to render the peptide fully active. We demonstrate that non-invasive, transdermal time-regulated activation of cell-adhesive RGD peptide on implanted biomaterials regulates in vivo cell adhesion, inflammation, fibrous encapsulation, and vascularization of the material. This work shows that triggered in vivo presentation of bioligands can be harnessed to direct tissue reparative responses associated with implanted biomaterials.

Bioengineering approaches to guide stem cell-based organogenesis

During organogenesis, various molecular and physical signals are orchestrated in space and time to sculpt multiple cell types into functional tissues and organs. The complex and dynamic nature of the process has hindered studies aimed at delineating morphogenetic mechanisms in vivo, particularly in mammals. Recent demonstrations of stem cell-driven tissue assembly in culture offer a powerful new tool for modeling and dissecting organogenesis. However, despite the highly organotypic nature of stem cell-derived tissues, substantial differences set them apart from their in vivo counterparts, probably owing to the altered microenvironment in which they reside and the lack of mesenchymal influences. Advances in the biomaterials and microtechnology fields have, for example, afforded a high degree of spatiotemporal control over the cellular microenvironment, making it possible to interrogate the effects of individual microenvironmental components in a modular fashion and rapidly identify organ-specific synthetic culture models. Hence, bioengineering approaches promise to bridge the gap between stem cell-driven tissue formation in culture and morphogenesis in vivo, offering mechanistic insight into organogenesis and unveiling powerful new models for drug discovery, as well as strategies for tissue regeneration in the clinic. We draw on several examples of stem cell-derived organoids to illustrate how bioengineering can contribute to tissue formation ex vivo. We also discuss the challenges that lie ahead and potential ways to overcome them.

Drug discovery through stem cell-based organoid models

The development of new drugs is currently a long and costly process in large part due to the failure of promising drug candidates identified in initial in vitro screens to perform as intended in vivo. New approaches to drug screening are being developed which focus on providing more biomimetic platforms. This review surveys this new generation of drug screening technologies, and provides an overview of recent developments in organoid culture systems which could afford previously unmatched fidelity for testing bioactivity and toxicity. The challenges inherent in such approaches will also be discussed, with a view towards bridging the gap between proof-of-concept studies and a wider implementation within the drug development community.

Quantification and modeling of stem cell-niche interaction

Adult stem cells persist lifelong in the organism, where they are responsible for tissue homeostasis and repair. It is commonly assumed that their maintenance and function are facilitated in local environments called "stem cell niches." Although there is convincing evidence that a variety of niche components determine stem cell fate, the regulatory details of stem cell-niche interactions are widely unknown. To pave the way for a substantiated discussion of these interactions, we first focus on the stem cells themselves and describe the stem cell defining criteria and their implications. The fate of the cells that fulfill these criteria is regulated by a broad spectrum of factors and regulatory mechanisms. A summary of established components and their action is given exemplary for the hematopoietic system. The complexity resulting from the interplay of various cell types, signaling molecules, and extracellular structures can be boiled down to important key features as exemplified by the presented model of hematopoietic stem cell organization. Although neglecting many details, we show that this and similar models have the power to yield intriguing results as proven by the agreement of the presented model with experimental data and the predictions derived from model simulations. Finally, we will discuss the paradigm of systems biology and give a summary of the techniques that promise to unveil further details of the organization principles of stem cell niches at different levels. The synergistic effect of the described techniques together with the integration of their results into a unified model that allows quantitative evaluation and predictions may lead to a better and more systematic understanding of the most relevant niche elements and their interactions.

Engineered micromechanical cues affecting human pluripotent stem cell regulations and fate

The survival, growth, self-renewal, and differentiation of human pluripotent stem cells (hPSCs) are influenced by their microenvironment, or so-called "niche," consisting of particular chemical and physical cues. Previous studies on mesenchymal stem cells and other stem cells have collectively uncovered the importance of physical cues and have begun to shed light on how stem cells sense and process such cues. In an attempt to support similar progress in mechanobiology of hPSCs, we review mechanosensory machinery, which plays an important role in cell-extracellular matrix interactions, cell-cell interactions, and subsequent intracellular responses. In addition, we review recent studies on the mechanobiology of hPSCs, in which engineered micromechanical environments were used to investigate effects of specific physical cues. Identifying key physical cues and understanding their mechanism will ultimately help in harnessing the full potential of hPSCs for clinical applications.

Regeneration-on-a-chip? The perspectives on use of microfluidics in regenerative medicine

The aim of regenerative medicine is to restore or establish normal function of damaged tissues or organs. Tremendous efforts are placed into development of novel regenerative strategies, involving (stem) cells, soluble factors, biomaterials or combinations thereof, as a result of the growing need caused by continuous population aging. To satisfy this need, fast and reliable assessment of (biological) performance is sought, not only to select the potentially interesting candidates, but also to rule out poor ones at an early stage of development. Microfluidics may provide a new avenue to accelerate research and development in the field of regenerative medicine as it has proven its maturity for the realization of high-throughput screening platforms. In addition, microfluidic systems offer other advantages such as the possibility to create in vivo-like microenvironments. Besides the complexity of organs or tissues that need to be regenerated, regenerative medicine brings additional challenges of complex regeneration processes and strategies. The question therefore arises whether so much complexity can be integrated into microfluidic systems without compromising reliability and throughput of assays. With this review, we aim to investigate whether microfluidics can become widely applied in regenerative medicine research and/or strategies.

Directed neural differentiation of induced pluripotent stem cells from non-human primates

Induced pluripotent stem cells (iPS cells) are important for the future development of regenerative medicine involving autologous cell therapy. Before autologous cell therapy can be applied to human patients, suitable animal models must be developed, and in this context non-human primate models are critical. We previously characterized several lines of marmoset iPS cells derived from newborn skin fibroblasts. In the present studies, we explored methods for the directed differentiation of marmoset iPS cells in the neuroectodermal lineage. In this process we used an iterative process in which combinations of small molecules and protein factors were tested for their effects on mRNA levels of genes that are markers for the neuroectodermal lineage. This iterative process identified combinations of chemicals/factors that substantially improved the degree of marker gene expression over the initially tested combinations. This approach should be generally valuable in the directed differentiation of pluripotent cells for experimental cell therapy.

Stem cell modeling: From gene networks to cell populations

Despite rapid advances in the field of stem/progenitor cells through experimental studies, relevant modeling approaches have not progressed with a similar pace. Various models have focused on particular aspects of stem cell physiology including gene regulatory networks, gene expression noise and signaling cascades activated by exogenous factors. However, the self-renewal and differentiation of stem cells is driven by the coordinated regulation of events at the subcellular, intercellular and milieu levels. Such events also span multiple time domains from the fast molecular reactions governing gene expression to the slower cell cycle and division. Thus, the development of multiscale computational frameworks for stem cell populations is highly desirable. Multiscale models are expected to aid the design of efficient differentiation strategies and bioprocesses for the generation of therapeutically useful stem cell progeny. Yet, challenges in making these models tractable and pairing those to sufficient experimental data prevent their wide adoption by the stem cell community. Here, we review modeling approaches reported for stem cell populations and associated hurdles.

Microarrayed Materials for Stem Cells

Stem cells hold remarkable promise for applications in disease modeling, cancer therapy and regenerative medicine. Despite the significant progress made during the last decade, designing materials to control stem cell fate remains challenging. As an alternative, materials microarray technology has received great attention because it allows for high throughput materials synthesis and screening at a reasonable cost. Here, we discuss recent developments in materials microarray technology and their applications in stem cell engineering. Future opportunities in the field will also be reviewed.

Computational multiscale modeling of embryo development

Recent advances in live imaging and genetics of mammalian development which integrate observations of biochemical activity, cell-cell signaling and mechanical interactions between cells pave the way for predictive mathematical multi-scale modeling. In early mammalian embryo development, two of the most critical events which lead to tissue patterning involve changes in gene expression as well as mechanical interactions between cells. We discuss the relevance of mathematical modeling of multi-cellular systems and in particular in simulating these patterns and describe some of the technical challenges one encounters. Many of these issues are not unique for the embryonic system but are shared by other multi-cellular modeling areas.

Interface biology of implants

To successfully apply implant materials for regenerative processes in the body, understanding the mechanisms at the interface between cells or tissues and the artificial material is of critical importance. This topic is becoming increasing relevant for clinical applications. For the fourth time, around 200 scientists met in Rostock, Germany for the international symposium "Interface Biology of Implants". The aim of the symposium is to promote interdisciplinary dialogue between scientists from different disciplines. The symposium also emphasizes the need of this applied scientific field for permanent input from basic sciences.