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Biomedicines
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Organoids in Biomedical Research
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Organoids in Biomedical Research

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Biomedical Engineering and Materials".

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 6547

Special Issue Editor

Dr. Ahmad Salti

E-Mail Website
Guest Editor
Center for Medical Research, University Clinic for Ophthalmology and Optometry, Johannes Kepler University Linz, 4020 Linz, Austria
Interests: induced pluripotent stem cells (iPSCs); retinal organoids; brain organoids; neurodegenerative diseases; retinitis pigmentosa; Parkinson’s disease; in vitro models; brain development

Special Issue Information

Dear Colleagues,

Organoids are three-dimensional (3D) self-organized in vitro replicas of specific organs or tissues. These miniature structures can be generated from either human pluripotent stem cells or adult stem cells derived from healthy individuals or patients. Three-dimensional organoids represent a compelling new class of biological models because they resemble the original organs and carry genetic information that can recapitulate human (patho)physiology. Therefore, organoids carry great promise for biomedical research because they can be utilized for various applications, such as preclinical drug testing, personalized and regenerative medicine, gene repair and transplantation. Extensive research is currently being conducted to generate various types of organoids, including brain, retinal, cardiac, intestinal and many others.

This Special Issue, “Organoids in Biomedical Research”, aims to provide the latest insights into the generation, characterization, and application of 3D organoids as human models for biomedical research. The main focus will be on brain and retinal organoids to model neurodegenerative and retinal diseases.

Dr. Ahmad Salti
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomedicines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • three-dimensional organoids
  • pluripotent stem cells
  • in vitro models
  • disease modeling
  • neurodegenerative diseases
  • retinal diseases
  • drug testing
  • regenerative medicine
  • gene repair
  • transplantation

Published Papers (4 papers)

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Research

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16 pages, 778 KiB  
Article
Mu-Net a Light Architecture for Small Dataset Segmentation of Brain Organoid Bright-Field Images
by Clara Brémond Martin, Camille Simon Chane, Cédric Clouchoux and Aymeric Histace
Biomedicines 2023, 11(10), 2687; https://doi.org/10.3390/biomedicines11102687 - 30 Sep 2023
Viewed by 1009
Abstract
To characterize the growth of brain organoids (BOs), cultures that replicate some early physiological or pathological developments of the human brain are usually manually extracted. Due to their novelty, only small datasets of these images are available, but segmenting the organoid shape automatically [...] Read more.
To characterize the growth of brain organoids (BOs), cultures that replicate some early physiological or pathological developments of the human brain are usually manually extracted. Due to their novelty, only small datasets of these images are available, but segmenting the organoid shape automatically with deep learning (DL) tools requires a larger number of images. Light U-Net segmentation architectures, which reduce the training time while increasing the sensitivity under small input datasets, have recently emerged. We further reduce the U-Net architecture and compare the proposed architecture (MU-Net) with U-Net and UNet-Mini on bright-field images of BOs using several data augmentation strategies. In each case, we perform leave-one-out cross-validation on 40 original and 40 synthesized images with an optimized adversarial autoencoder (AAE) or on 40 transformed images. The best results are achieved with U-Net segmentation trained on optimized augmentation. However, our novel method, MU-Net, is more robust: it achieves nearly as accurate segmentation results regardless of the dataset used for training (various AAEs or a transformation augmentation). In this study, we confirm that small datasets of BOs can be segmented with a light U-Net method almost as accurately as with the original method. Full article
(This article belongs to the Special Issue Organoids in Biomedical Research)
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Review

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13 pages, 996 KiB  
Review
Organoids Modeling Stroke in a Petri Dish
by Chiara Giorgi, Vanessa Castelli, Michele d’Angelo and Annamaria Cimini
Biomedicines 2024, 12(4), 877; https://doi.org/10.3390/biomedicines12040877 - 16 Apr 2024
Viewed by 459
Abstract
Stroke is a common neurological disorder, the second leading cause of death, and the third leading cause of disability. Unfortunately, the only approved drug for it is tissue plasminogen, but the therapeutic window is limited. In this context, preclinical studies are relevant to [...] Read more.
Stroke is a common neurological disorder, the second leading cause of death, and the third leading cause of disability. Unfortunately, the only approved drug for it is tissue plasminogen, but the therapeutic window is limited. In this context, preclinical studies are relevant to better dissect the underlying mechanisms of stroke and for the drug screening of potential therapies. Brain organoids could be relevant in this setting. They are derived from pluripotent stem cells or isolated organ progenitors that differentiate to form an organ-like tissue, exhibiting multiple cell types that self-organize to form a structure not unlike the organ in vivo. Brain organoids mimic many key features of early human brain development at molecular, cellular, structural, and functional levels and have emerged as novel model systems that can be used to investigate human brain diseases including stroke. Brain organoids are a promising and powerful tool for ischemic stroke studies; however, there are a few concerns that need to be addressed, including the lack of vascularization and the many cell types that are typically present in the human brain. The aim of this review is to discuss the potential of brain organoids as a novel model system for studying ischemic stroke, highlighting both the advantages and disadvantages in the use of this technology. Full article
(This article belongs to the Special Issue Organoids in Biomedical Research)
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20 pages, 1316 KiB  
Review
Alveolar Type 2 Epithelial Cell Organoids: Focus on Culture Methods
by Krishan Gopal Jain, Nan Miles Xi, Runzhen Zhao, Waqas Ahmad, Gibran Ali and Hong-Long Ji
Biomedicines 2023, 11(11), 3034; https://doi.org/10.3390/biomedicines11113034 - 12 Nov 2023
Cited by 1 | Viewed by 1745
Abstract
Lung diseases rank third in terms of mortality and represent a significant economic burden globally. Scientists have been conducting research to better understand respiratory diseases and find treatments for them. An ideal in vitro model must mimic the in vivo organ structure, physiology, [...] Read more.
Lung diseases rank third in terms of mortality and represent a significant economic burden globally. Scientists have been conducting research to better understand respiratory diseases and find treatments for them. An ideal in vitro model must mimic the in vivo organ structure, physiology, and pathology. Organoids are self-organizing, three-dimensional (3D) structures originating from adult stem cells, embryonic lung bud progenitors, embryonic stem cells (ESCs), and induced pluripotent stem cells (iPSCs). These 3D organoid cultures may provide a platform for exploring tissue development, the regulatory mechanisms related to the repair of lung epithelia, pathophysiological and immunomodulatory responses to different respiratory conditions, and screening compounds for new drugs. To create 3D lung organoids in vitro, both co-culture and feeder-free methods have been used. However, there exists substantial heterogeneity in the organoid culture methods, including the sources of AT2 cells, media composition, and feeder cell origins. This article highlights the currently available methods for growing AT2 organoids and prospective improvements to improve the available culture techniques/conditions. Further, we discuss various applications, particularly those aimed at modeling human distal lung diseases and cell therapy. Full article
(This article belongs to the Special Issue Organoids in Biomedical Research)
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12 pages, 918 KiB  
Review
The Role of Patient-Derived Organoids in Triple-Negative Breast Cancer Drug Screening
by Iason Psilopatis, Amalia Mantzari, Kleio Vrettou and Stamatios Theocharis
Biomedicines 2023, 11(3), 773; https://doi.org/10.3390/biomedicines11030773 - 03 Mar 2023
Cited by 2 | Viewed by 2511
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer subtypes, with a grave prognosis and few effective treatment options. Organoids represent revolutionary three-dimensional cell culture models, derived from stem or differentiated cells and preserving the capacity to differentiate into the [...] Read more.
Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer subtypes, with a grave prognosis and few effective treatment options. Organoids represent revolutionary three-dimensional cell culture models, derived from stem or differentiated cells and preserving the capacity to differentiate into the cell types of their tissue of origin. The current review aims at studying the potential of patient-derived TNBC organoids for drug sensitivity testing as well as highlighting the advantages of the organoid technology in terms of drug screening. In order to identify relevant studies, a literature review was conducted using the MEDLINE and LIVIVO databases. The search terms “organoid” and “triple-negative breast cancer” were employed, and we were able to identify 25 studies published between 2018 and 2022. The current manuscript represents the first comprehensive review of the literature focusing on the use of patient-derived organoids for drug sensitivity testing in TNBC. Patient-derived organoids are excellent in vitro study models capable of promoting personalized TNBC therapy by reflecting the treatment responses of the corresponding patients and exhibiting high predictive value in the context of patient survival evaluation. Full article
(This article belongs to the Special Issue Organoids in Biomedical Research)
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