Organoids for Drug Discovery and Personalized Medicine

Development of Prostate Cancer Organoid Culture Models in Basic Medicine and Translational Research

Prostate cancer (PC) is the most prevalent cancer in men and the second main cause of cancer-related death in Western society. The lack of proper PC models that recapitulate the molecular and genomic landscape of clinical disease has hampered progress toward translational research to understand the disease initiation, progression, and therapeutic responses in each patient. Although several models have been developed, they hardly emulated the complicated PC microenvironment. Precision medicine is an emerging approach predicting appropriate therapies for individual cancer patients by means of various analyses of individual genomic profiling and targeting specific cancer pathways. In PC, precision medicine also has the potential to impose changes in clinical practices. Here, we describe the various PC models with special focus on PC organoids and their values in basic medicine, personalized therapy, and translational researches in vitro and in vivo, which could help to achieve the full transformative power of cancer precision medicine.

Stem Cell Signaling Pathways in the Small Intestine

The ability of stem cells to divide and differentiate is necessary for tissue repair and homeostasis. Appropriate spatial and temporal mechanisms are needed. Local intercellular signaling increases expression of specific genes that mediate and maintain differentiation. Diffusible signaling molecules provide concentration-dependent induction of specific patterns of cell types or regions. Differentiation of adjacent cells, on the other hand, requires cell–cell contact and subsequent signaling. These two types of signals work together to allow stem cells to provide what organisms require. The ability to grow organoids has increased our understanding of the cellular and molecular features of small “niches” that modulate stem cell function in various organs, including the small intestine.

The challenge of developing human 3D organoids into medicines

The capacity of organoids to generate complex 3D structures resembling organs is revolutionizing the fields of developmental and stem cell biology. We are currently establishing the foundations for translational applications of organoids such as drug screening, personalized medicine and launching the future of cell therapy using organoids. However, clinical translation of organoids into cell replacement therapies is halted due to (A) a few preclinical studies demonstrating their efficacy and (B) the lack of robust, reproducible, and scalable methods of production in compliance with current pharmaceutical standards. In this issue of Stem Cell Research & Therapy [ref], Dossena and collaborators present a validated bioprocess design for large-scale production of human pancreatic organoids from cadaveric tissue in accordance with current good manufacturing practice. The authors also propose a set of specifications of starting materials and critical quality attributes of final products that are of interest to other developments provided that this type of medicines are different than any other medicinal product due to their complex composition and living nature of the active ingredient. Although large-scale production of functional cells secreting insulin is still a challenge, the development of methods such as the one presented by Dossena and collaborators contributes to move toward clinical use of organoids in the treatment of type 1 diabetes and opens avenues for future clinical use of organoids in degenerative pathologies.

Harnessing the Potential of Stem Cells for Disease Modeling: Progress and Promises

Ex vivo cell/tissue-based models are an essential step in the workflow of pathophysiology studies, assay development, disease modeling, drug discovery, and development of personalized therapeutic strategies. For these purposes, both scientific and pharmaceutical research have adopted ex vivo stem cell models because of their better predictive power. As matter of a fact, the advancing in isolation and in vitro expansion protocols for culturing autologous human stem cells, and the standardization of methods for generating patient-derived induced pluripotent stem cells has made feasible to generate and investigate human cellular disease models with even greater speed and efficiency. Furthermore, the potential of stem cells on generating more complex systems, such as scaffold-cell models, organoids, or organ-on-a-chip, allowed to overcome the limitations of the two-dimensional culture systems as well as to better mimic tissues structures and functions. Finally, the advent of genome-editing/gene therapy technologies had a great impact on the generation of more proficient stem cell-disease models and on establishing an effective therapeutic treatment. In this review, we discuss important breakthroughs of stem cell-based models highlighting current directions, advantages, and limitations and point out the need to combine experimental biology with computational tools able to describe complex biological systems and deliver results or predictions in the context of personalized medicine.

Advanced Bottom-Up Engineering of Living Architectures

Bottom-up tissue engineering is a promising approach for designing modular biomimetic structures that aim to recapitulate the intricate hierarchy and biofunctionality of native human tissues. In recent years, this field has seen exciting progress driven by an increasing knowledge of biological systems and their rational deconstruction into key core components. Relevant advances in the bottom-up assembly of unitary living blocks toward the creation of higher order bioarchitectures based on multicellular-rich structures or multicomponent cell-biomaterial synergies are described. An up-to-date critical overview of long-term existing and rapidly emerging technologies for integrative bottom-up tissue engineering is provided, including discussion of their practical challenges and required advances. It is envisioned that a combination of cell-biomaterial constructs with bioadaptable features and biospecific 3D designs will contribute to the development of more robust and functional humanized tissues for therapies and disease models, as well as tools for fundamental biological studies.

Roles of nAChR and Wnt signaling in intestinal stem cell function and inflammation

Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels that signal using endogenous acetylcholine (ACh) and the agonist, nicotine. The nAChR signaling pathway is a central regulator of physiological homeostasis in the central and peripheral nervous systems. The receptors are expressed not only in the nervous system, but also play a pivotal role in regulation of epithelial cell growth, migration, differentiation, and inflammation processes in various mammalian non-neuronal cells. In the intestine, the Wnt signaling pathway plays a central role in the epithelium and is a principal regulator of intestinal stem cell (ISC) identity and proliferation. Since Wnt signaling was first described more than 40 years ago in ISCs, large amounts of scientific evidence have demonstrated remarkable long-term self-renewal capacity of ISCs. Intestinal organoids are commonly used for studying ISC biology and intestinal pathophysiology. The contribution of non-neuronal nAChR signaling to Wnt signaling in the intestine has received less attention. Experiments using cultured intestinal organoids that lack nerve and immune cells were performed. Endogenous ACh is synthesized in the intestinal epithelium and drives organoid growth and differentiation through activation of nAChR signaling. Furthermore, nAChR signaling is coordinated with Wnt signaling for regulation of ISC function. Elucidating the mechanism of the coordinated activities of nAChR and Wnt signaling in the intestine provides new insight into epithelial homeostasis, and may be of particular relevance in inflammatory bowel diseases such as ulcerative colitis and Crohn's disease.

Tissue Engineering for Musculoskeletal Regeneration and Disease Modeling

Musculoskeletal injuries and associated conditions are the leading cause of physical disability worldwide. The concept of tissue engineering has opened up novel approaches to repair musculoskeletal defects in a fast and/or efficient manner. Biomaterials, cells, and signaling molecules constitute the tissue engineering triad. In the past 40 years, significant progress has been made in developing and optimizing all three components, but only a very limited number of technologies have been successfully translated into clinical applications. A major limiting factor of this barrier to translation is the insufficiency of two-dimensional cell cultures and traditional animal models in informing the safety and efficacy of in-human applications. In recent years, microphysiological systems, often referred to as organ or tissue chips, generated according to tissue engineering principles, have been proposed as the next-generation drug testing models. This chapter aims to first review the current tissue engineering-based approaches that are being applied to fabricate and develop the individual critical elements involved in musculoskeletal organ/tissue chips. We next highlight the general strategy of generating musculoskeletal tissue chips and their potential in future regenerative medicine research. Exemplary microphysiological systems mimicking musculoskeletal tissues are described. With sufficient physiological accuracy and relevance, the human cell-derived, three-dimensional, multi-tissue systems have been used to model a number of orthopedic disorders and to test new treatments. We anticipate that the novel emerging tissue chip technology will continually reshape and improve our understanding of human musculoskeletal pathophysiology, ultimately accelerating the development of advanced pharmaceutics and regenerative therapies.

Therapies for rare diseases: therapeutic modalities, progress and challenges ahead

Most rare diseases still lack approved treatments despite major advances in research providing the tools to understand their molecular basis, as well as legislation providing regulatory and economic incentives to catalyse the development of specific therapies. Addressing this translational gap is a multifaceted challenge, for which a key aspect is the selection of the optimal therapeutic modality for translating advances in rare disease knowledge into potential medicines, known as orphan drugs. With this in mind, we discuss here the technological basis and rare disease applicability of the main therapeutic modalities, including small molecules, monoclonal antibodies, protein replacement therapies, oligonucleotides and gene and cell therapies, as well as drug repurposing. For each modality, we consider its strengths and limitations as a platform for rare disease therapy development and describe clinical progress so far in developing drugs based on it. We also discuss selected overarching topics in the development of therapies for rare diseases, such as approval statistics, engagement of patients in the process, regulatory pathways and digital tools.

Intestinal enteroids/organoids: A novel platform for drug discovery in inflammatory bowel diseases

The introduction of biologics such as anti-tumor necrosis factor (TNF) monoclonal antibodies followed by anti-integrins has dramatically changed the therapeutic paradigm of inflammatory bowel diseases (IBD). Furthermore, a newly developed anti-p40 subunit of interleukin (IL)-12 and IL-23 (ustekinumab) has been recently approved in the United States for patients with moderate to severe Crohn’s disease who have failed treatment with anti-TNFs. However, these immunosuppressive therapeutics which focus on anti-inflammatory mechanisms or immune cells still fail to achieve long-term remission in a significant percentage of patients. This strongly underlines the need to identify novel treatment targets beyond immune suppression to treat IBD. Recent studies have revealed the critical role of intestinal epithelial cells (IECs) in the pathogenesis of IBD. Physical, biochemical and immunologic driven barrier dysfunctions of epithelial cells contribute to the development of IBD. In addition, the recent establishment of adult stem cell-derived intestinal enteroid/organoid culture technology has allowed an exciting opportunity to study human IECs comprising all normal epithelial cells. This long-term epithelial culture model can be generated from endoscopic biopsies or surgical resections and recapitulates the tissue of origin, representing a promising platform for novel drug discovery in IBD. This review describes the advantages of intestinal enteroids/organoids as a research tool for intestinal diseases, introduces studies with these models in IBD, and gives a description of the current status of therapeutic approaches in IBD. Finally, we provide an overview of the current endeavors to identify a novel drug target for IBD therapy based on studies with human enteroids/organoids and describe the challenges in using enteroids/organoids as an IBD model.

Establishment of a novel experimental model for muscle-invasive bladder cancer using a dog bladder cancer organoid culture

In human and dogs, bladder cancer (BC) is the most common neoplasm affecting the urinary tract. Dog BC resembles human muscle‐invasive BC in histopathological characteristics and gene expression profiles, and could be an important research model for this disease. Cancer patient‐derived organoid culture can recapitulate organ structures and maintains the gene expression profiles of original tumor tissues. In a previous study, we generated dog prostate cancer organoids using urine samples, however dog BC organoids had never been produced. Therefore we aimed to generate dog BC organoids using urine samples and check their histopathological characteristics, drug sensitivity, and gene expression profiles. Organoids from individual BC dogs were successfully generated, expressed urothelial cell markers (CK7, CK20, and UPK3A) and exhibited tumorigenesis in vivo. In a cell viability assay, the response to combined treatment with a range of anticancer drugs (cisplatin, vinblastine, gemcitabine or piroxicam) was markedly different in each BC organoid. In RNA‐sequencing analysis, expression levels of basal cell markers (CK5 and DSG3) and several novel genes (MMP28,CTSE,CNN3,TFPI2,COL17A1, and AGPAT4) were upregulated in BC organoids compared with normal bladder tissues or two‐dimensional (2D) BC cell lines. These established dog BC organoids might be a useful tool, not only to determine suitable chemotherapy for BC diseased dogs but also to identify novel biomarkers in human muscle‐invasive BC. In the present study, for the 1st time, dog BC organoids were generated and several specifically upregulated organoid genes were identified. Our data suggest that dog BC organoids might become a new tool to provide fresh insights into both dog BC therapy and diagnostic biomarkers.

Proteomics in the World of Induced Pluripotent Stem Cells

Omics approaches have significantly impacted knowledge about molecular signaling pathways driving cell function. Induced pluripotent stem cells (iPSC) have revolutionized the field of biological sciences and proteomics and, in particular, has been instrumental in identifying key elements operating during the maintenance of the pluripotent state and the differentiation process to the diverse cell types that form organisms. This review covers the evolution of conceptual and methodological strategies in proteomics; briefly describes the generation of iPSC from a historical perspective, the state-of-the-art of iPSC-based proteomics; and compares data on the proteome and transcriptome of iPSC to that of embryonic stem cells (ESC). Finally, proteomics of healthy and diseased cells and organoids differentiated from iPSC are analyzed.

L’édition de gènes dans la découverte du médicament et l’innovation thérapeutique

On lit régulièrement dans la presse que les méthodes thérapeutiques récentes vont supplanter celles plus traditionnelles de la pharmacopée. Le biomédicament et les thérapies géniques connaissent un essor considérable, mais on s’aperçoit que chaque approche thérapeutique a ses contraintes et ses limites et que les champs thérapeutiques les plus pertinents sont le plus souvent complémentaires de ceux du médicament traditionnel, plutôt que concurrents, et bien souvent synergiques. Cette revue met en perspective les méthodes de l’édition de génomes avec celle de la découverte du médicament, dans le domaine de l’innovation thérapeutique.