In vitro models of the human esophagus reveal ancestrally diverse response to injury

European Americans (EA) are more susceptible to esophageal tissue damage and inflammation when exposed to gastric acid and bile acid reflux and have a higher incidence of esophageal adenocarcinoma when compared to African Americans (AA). Population studies have implicated specific genes for these differences; however, the underlying cause for these differences is not well understood. We describe a robust long-term culture system to grow primary human esophagus in vitro, use single cell RNA sequencing to compare primary human biopsies to their in vitro counterparts, identify known and new molecular markers of basal cell types, and demonstrate that in vivo cellular heterogeneity is maintained in vitro. We further developed an ancestrally diverse biobank and a high-content, image based, screening assay to interrogate bile-acid injury response. These results demonstrated that AA esophageal cells responded significantly differently than EA-derived cells, mirroring clinical findings, having important implications for addressing disparities in early drug development pipelines.

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Modelling the Human Placental Interface In Vitro—A Review

Micromachines ◽

10.3390/mi12080884 ◽

2021 ◽

Vol 12 (8) ◽

pp. 884

Author(s):

Marta Cherubini ◽

Scott Erickson ◽

Kristina Haase

Keyword(s):

Drug Testing ◽

Cell Types ◽

In Vitro Models ◽

Placental Development ◽

Scientific Challenge ◽

Induced Pluripotent ◽

And Function ◽

And Control

Acting as the primary link between mother and fetus, the placenta is involved in regulating nutrient, oxygen, and waste exchange; thus, healthy placental development is crucial for a successful pregnancy. In line with the increasing demands of the fetus, the placenta evolves throughout pregnancy, making it a particularly difficult organ to study. Research into placental development and dysfunction poses a unique scientific challenge due to ethical constraints and the differences in morphology and function that exist between species. Recently, there have been increased efforts towards generating in vitro models of the human placenta. Advancements in the differentiation of human induced pluripotent stem cells (hiPSCs), microfluidics, and bioprinting have each contributed to the development of new models, which can be designed to closely match physiological in vivo conditions. By including relevant placental cell types and control over the microenvironment, these new in vitro models promise to reveal clues to the pathogenesis of placental dysfunction and facilitate drug testing across the maternal–fetal interface. In this minireview, we aim to highlight current in vitro placental models and their applications in the study of disease and discuss future avenues for these in vitro models.

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Production of Human Pluripotent Stem Cell-Derived Hepatic Cell Lineages and Liver Organoids: Current Status and Potential Applications

Bioengineering ◽

10.3390/bioengineering7020036 ◽

2020 ◽

Vol 7 (2) ◽

pp. 36 ◽

Cited By ~ 5

Author(s):

João P. Cotovio ◽

Tiago G. Fernandes

Keyword(s):

Cell Types ◽

In Vitro Models ◽

Hepatic Cell ◽

Current Status ◽

Organ Shortage ◽

Cell Lineages ◽

Potential Applications ◽

Liver Organoids

Liver disease is one of the leading causes of death worldwide, leading to the death of approximately 2 million people per year. Current therapies include orthotopic liver transplantation, however, donor organ shortage remains a great challenge. In addition, the development of novel therapeutics has been limited due to the lack of in vitro models that mimic in vivo liver physiology. Accordingly, hepatic cell lineages derived from human pluripotent stem cells (hPSCs) represent a promising cell source for liver cell therapy, disease modelling, and drug discovery. Moreover, the development of new culture systems bringing together the multiple liver-specific hepatic cell types triggered the development of hPSC-derived liver organoids. Therefore, these human liver-based platforms hold great potential for clinical applications. In this review, the production of the different hepatic cell lineages from hPSCs, including hepatocytes, as well as the emerging strategies to generate hPSC-derived liver organoids will be assessed, while current biomedical applications will be highlighted.

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Microphysiological Systems: A Pathologist’s Perspective

Veterinary Pathology ◽

10.1177/0300985820908794 ◽

2020 ◽

Vol 57 (3) ◽

pp. 358-368

Author(s):

Radhakrishna Sura ◽

Terry Van Vleet ◽

Brian R. Berridge

Keyword(s):

Drug Discovery ◽

Biomedical Research ◽

Interdisciplinary Collaboration ◽

Cell Types ◽

In Vitro Models ◽

In Vitro Methods ◽

Microphysiological Systems ◽

Regulatory Acceptance

High-throughput in vitro models lack human-relevant complexity, which undermines their ability to accurately mimic in vivo biologic and pathologic responses. The emergence of microphysiological systems (MPS) presents an opportunity to revolutionize in vitro modeling for both basic biomedical research and applied drug discovery. The MPS platform has been an area of interdisciplinary collaboration to develop new, predictive, and reliable in vitro methods for regulatory acceptance. The current MPS models have been developed to recapitulate an organ or tissue on a smaller scale. However, the complexity of these models (ie, including all cell types present in the in vivo tissue) with appropriate structural, functional, and biochemical attributes are often not fully characterized. Here, we provide an overview of the capabilities and limitations of the microfluidic MPS model (aka organs-on-chips) within the scope of drug development. We recommend the engagement of pathologists early in the MPS design, characterization, and validation phases, because this will enable development of more robust and comprehensive MPS models that can accurately replicate normal biology and pathophysiology and hence be more predictive of human responses.

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Robust and Scalable Angiogenesis Assay of Perfused 3D Human iPSC-Derived Endothelium for Anti-Angiogenic Drug Screening

International Journal of Molecular Sciences ◽

10.3390/ijms21134804 ◽

2020 ◽

Vol 21 (13) ◽

pp. 4804

Author(s):

Vincent van Duinen ◽

Wendy Stam ◽

Eva Mulder ◽

Farbod Famili ◽

Arie Reijerkerk ◽

...

Keyword(s):

Drug Screening ◽

Cell Formation ◽

Cell Types ◽

Culture Conditions ◽

In Vitro Assays ◽

Vegf Receptor ◽

Screening Assay ◽

Angiogenesis Assay

To advance pre-clinical vascular drug research, in vitro assays are needed that closely mimic the process of angiogenesis in vivo. Such assays should combine physiological relevant culture conditions with robustness and scalability to enable drug screening. We developed a perfused 3D angiogenesis assay that includes endothelial cells (ECs) from induced pluripotent stem cells (iPSC) and assessed its performance and suitability for anti-angiogenic drug screening. Angiogenic sprouting was compared with primary ECs and showed that the microvessels from iPSC-EC exhibit similar sprouting behavior, including tip cell formation, directional sprouting and lumen formation. Inhibition with sunitinib, a clinically used vascular endothelial growth factor (VEGF) receptor type 2 inhibitor, and 3-(3-pyridinyl)-1-(4-pyridinyl)-2-propen-1-one (3PO), a transient glycolysis inhibitor, both significantly reduced the sprouting of both iPSC-ECs and primary ECs, supporting that both cell types show VEGF gradient-driven angiogenic sprouting. The assay performance was quantified for sunitinib, yielding a minimal signal window of 11 and Z-factor of at least 0.75, both meeting the criteria to be used as screening assay. In conclusion, we have developed a robust and scalable assay that includes physiological relevant culture conditions and is amenable to screening of anti-angiogenic compounds.

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Mesenchymal Stem Cells as a Promising Cell Source for Integration in Novel In Vitro Models

Biomolecules ◽

10.3390/biom10091306 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1306

Author(s):

Ann-Kristin Afflerbach ◽

Mark D. Kiri ◽

Tahir Detinis ◽

Ben M. Maoz

Keyword(s):

Stem Cells ◽

Mesenchymal Stem Cells ◽

Cell Types ◽

In Vitro Models ◽

Cell Source ◽

Fundamental Research ◽

Multiple Cell ◽

Vitro Model

The human-relevance of an in vitro model is dependent on two main factors—(i) an appropriate human cell source and (ii) a modeling platform that recapitulates human in vivo conditions. Recent years have brought substantial advancements in both these aspects. In particular, mesenchymal stem cells (MSCs) have emerged as a promising cell source, as these cells can differentiate into multiple cell types, yet do not raise the ethical and practical concerns associated with other types of stem cells. In turn, advanced bioengineered in vitro models such as microfluidics, Organs-on-a-Chip, scaffolds, bioprinting and organoids are bringing researchers ever closer to mimicking complex in vivo environments, thereby overcoming some of the limitations of traditional 2D cell cultures. This review covers each of these advancements separately and discusses how the integration of MSCs into novel in vitro platforms may contribute enormously to clinical and fundamental research.

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Shared Nucleotide Flanks Confer Transcriptional Competency to bZip Core Motifs

10.1101/262659 ◽

2018 ◽

Author(s):

Daniel M. Cohen ◽

Hee-Woong Lim ◽

Kyoung-Jae Won ◽

David J. Steger

Keyword(s):

Binding Sites ◽

Cell Types ◽

In Vitro Models ◽

Strongly Correlated ◽

Core Motif ◽

Resolution Mapping ◽

Dna Specificity ◽

Dna Shape

ABSTRACTSequence-specific DNA binding recruits transcription factors (TFs) to the genome to regulate gene expression. Here, we perform high resolution mapping of CEBP proteins to determine how sequence dictates genomic occupancy. We demonstrate a fundamental difference between the sequence repertoire utilized by CEBPs in vivo versus the palindromic sequence preference reported by classical in vitro models, by identifying a palindromic motif at less than 1% of the genomic binding sites. On the native genome, CEBPs bind a diversity of related 10 bp sequences resulting from the fusion of degenerate and canonical half-sites. Altered DNA specificity of CEBPs in cells occurs through heterodimerization with other bZip TFs, and approximately 40% of CEBP-binding sites in primary human cells harbor motifs characteristic of CEBP heterodimers. In addition, we uncover an important role for sequence bias at core-motif-flanking bases for CEBPs and demonstrate that flanking bases regulate motif function across mammalian bZip TFs. Favorable flanking bases confer efficient TF occupancy and transcriptional activity, and DNA shape may explain how the flanks alter TF binding. Importantly, motif optimization within the 10-mer is strongly correlated with cell-type-independent recruitment of CEBPβ, providing key insight into how sequence sub-optimization affects genomic occupancy of widely expressed CEBPs across cell types.

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An integrated analysis of myeloid cells identifies gaps in in vitro models of in vivo biology

10.1101/719237 ◽

2019 ◽

Cited By ~ 1

Author(s):

Nadia Rajab ◽

Paul W Angel ◽

Yidi Deng ◽

Jennifer Gu ◽

Vanta Jameson ◽

...

Keyword(s):

Dendritic Cells ◽

Stem Cell ◽

Myeloid Cell ◽

Cell Types ◽

In Vitro Models ◽

Integrated Analysis ◽

Dendritic Cell Subsets ◽

Cell Data

SummaryThe Stemformatics myeloid atlas is an integrated transcriptome atlas of human macrophages and dendritic cells that systematically compares freshly isolated tissue-resident, cultured, and stem-cell derived myeloid cell types. We identified two broad classes of tissue-resident macrophages with lung, gut and tumour-associated macrophages most similar to monocytes. Microglia, Kupffer cells and synovial macrophages shared similar profiles with each other, and with cultured macrophages. Pluripotent stem cell-derived macrophages were not reminiscent of fetal-derived cells. Instead, they were characterized by atypical expression of collagen and a highly efferocytotic phenotype. Likewise, Flt3L-derived cord blood dendritic cells were distinct from conventional dendritic cell subsets isolated from primary tissues and lacked expression of key pattern recognition receptors. Myeloid subsets were reproducible across different experimental series, showing the resource is a robust reference for new data. External users can annotate and benchmark their own samples, including annotation of myeloid single cell data at www.stemformatics.org/atlas/myeloid/.

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Transcytosis: Crossing Cellular Barriers

Physiological Reviews ◽

10.1152/physrev.00001.2003 ◽

2003 ◽

Vol 83 (3) ◽

pp. 871-932 ◽

Cited By ~ 387

Author(s):

PAMELA L. TUMA ◽

ANN L. HUBBARD

Keyword(s):

Cell Types ◽

In Vitro Models ◽

Vesicle Traffic ◽

Fundamental Process ◽

A Cell ◽

Multicellular Organisms ◽

Different Cell Types ◽

Transport Of Macromolecules

Tuma, Pamela L., and Ann L. Hubbard. Transcytosis: Crossing Cellular Barriers. Physiol Rev 83: 871–932, 2003; 10.1152/physrev.00001.2003.—Transcytosis, the vesicular transport of macromolecules from one side of a cell to the other, is a strategy used by multicellular organisms to selectively move material between two environments without altering the unique compositions of those environments. In this review, we summarize our knowledge of the different cell types using transcytosis in vivo, the variety of cargo moved, and the diverse pathways for delivering that cargo. We evaluate in vitro models that are currently being used to study transcytosis. Caveolae-mediated transcytosis by endothelial cells that line the microvasculature and carry circulating plasma proteins to the interstitium is explained in more detail, as is clathrin-mediated transcytosis of IgA by epithelial cells of the digestive tract. The molecular basis of vesicle traffic is discussed, with emphasis on the gaps and uncertainties in our understanding of the molecules and mechanisms that regulate transcytosis. In our view there is still much to be learned about this fundamental process.

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THE PROSPECTS FOR APPLICATION OF LACTOFERRIN AND ITS DERIVATIVES IN THE TREATMENT OF CANCER

Problems in oncology ◽

10.37469/0507-3758-2019-65-6-785-790 ◽

2019 ◽

Vol 65 (6) ◽

pp. 785-790

Author(s):

Veronika Zorina

Keyword(s):

Gene Therapy ◽

Synthetic Peptides ◽

Cell Types ◽

In Vitro Models ◽

The World ◽

Specific Receptors ◽

Methods Of Treatment ◽

Universal Protein

Annually more than 250 thousand deaths from malignant diseases are registered in Russia and 8 million - in the world. The effectiveness of traditional methods of treatment, as well as of monoclonal antibodies and gene therapy is limited in the case of resistant forms of cancer and hard to reach tumors. Lactoferrin (LF) is a universal protein with anticancer activity and cross-species biocompatibility, which modulates the immune response and the redox/antioxidant system. Due to the ability to interact not only with specific receptors, but also with signaling and endocytosis receptors, TLR on various cell types, LF can overcome tissue barriers. The therapeutic efficacy of lactoferrin, its cleavage products, and synthetic peptides against various types of malignant proliferation was demonstrated with in vivo and in vitro models. The prospects of using LF as an adjuvant before chemotherapy and radiotherapy and as a carrier for gene therapy of cancer were experimentally demonstrated. However, the results of clinical studies are few and require further study.

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Review of Design Considerations for Brain-on-a-Chip Models

Micromachines ◽

10.3390/mi12040441 ◽

2021 ◽

Vol 12 (4) ◽

pp. 441

Author(s):

Tiffany Cameron ◽

Tanya Bennet ◽

Elyn Rowe ◽

Mehwish Anwer ◽

Cheryl Wellington ◽

...

Keyword(s):

Brain Research ◽

Neurovascular Unit ◽

Cell Monolayer ◽

Cell Types ◽

In Vitro Models ◽

Research Field ◽

Design Development ◽

Organ On A Chip

In recent years, the need for sophisticated human in vitro models for integrative biology has motivated the development of organ-on-a-chip platforms. Organ-on-a-chip devices are engineered to mimic the mechanical, biochemical and physiological properties of human organs; however, there are many important considerations when selecting or designing an appropriate device for investigating a specific scientific question. Building microfluidic Brain-on-a-Chip (BoC) models from the ground-up will allow for research questions to be answered more thoroughly in the brain research field, but the design of these devices requires several choices to be made throughout the design development phase. These considerations include the cell types, extracellular matrix (ECM) material(s), and perfusion/flow considerations. Choices made early in the design cycle will dictate the limitations of the device and influence the end-point results such as the permeability of the endothelial cell monolayer, and the expression of cell type-specific markers. To better understand why the engineering aspects of a microfluidic BoC need to be influenced by the desired biological environment, recent progress in microfluidic BoC technology is compared. This review focuses on perfusable blood–brain barrier (BBB) and neurovascular unit (NVU) models with discussions about the chip architecture, the ECM used, and how they relate to the in vivo human brain. With increased knowledge on how to make informed choices when selecting or designing BoC models, the scientific community will benefit from shorter development phases and platforms curated for their application.

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