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Rezaei Z, Wang N, Yang Y, Govindaraj K, Velasco JJ, Martinez Blanco AD, Bae NH, Lee H, Shin SR. Enhancing organoid technology with carbon-based nanomaterial biosensors: Advancements, challenges, and future directions. Adv Drug Deliv Rev 2025; 222:115592. [PMID: 40324529 DOI: 10.1016/j.addr.2025.115592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Revised: 03/26/2025] [Accepted: 04/24/2025] [Indexed: 05/07/2025]
Abstract
Various carbon-based nanomaterials (CBNs) have been utilized to develop nano- and microscale biosensors that enable real-time and continuous monitoring of biochemical and biophysical changes in living biological systems. The integration of CBN-based biosensors into organoids has recently provided valuable insights into organoid development, disease modeling, and drug responses, enhancing their functionality and expanding their applications in diverse biomedical fields. These biosensors have been particularly transformative in studying neurological disorders, cardiovascular diseases, cancer progression, and liver toxicity, where precise, non-invasive monitoring is crucial for understanding pathophysiological mechanisms and assessing therapeutic efficacy. This review introduces intra- and extracellular biosensors incorporating CBNs such as graphene, carbon nanotubes (CNTs), graphene oxide (GO), reduced graphene oxide (rGO), carbon dots (CDs), and fullerenes. Additionally, it discusses strategies for improving the biocompatibility of CBN-based biosensors and minimizing their potential toxicity to ensure long-term organoid viability. Key challenges such as biosensor integration, data accuracy, and functional compatibility with specific organoid models are also addressed. Furthermore, this review highlights how CBN-based biosensors enhance the precision and relevance of organoid models in biomedical research, particularly in organ-specific applications such as brain-on-a-chip systems for neurodegenerative disease studies, liver-on-a-chip platforms for hepatotoxicity screening, and cardiac organoids for assessing cardiotoxicity in drug development. Finally, it explores how biosensing technologies could revolutionize personalized medicine by enabling high throughput drug screening, patient-specific disease modeling, and integrated sensing platforms for early diagnostics. By capturing current advancements and future directions, this review underscores the transformative potential of carbon-based nanotechnology in organoid research and its broader impact on medical science.
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Affiliation(s)
- Zahra Rezaei
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Niyou Wang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Yipei Yang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA; Department of Orthopedic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen 518000, China
| | - Kannan Govindaraj
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA; Department of Developmental Bioengineering, TechMed Centre, University of Twente, Drienerlolaan 5, Enschede 7522NB, the Netherlands
| | - Jose Joaquin Velasco
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA; Monterrey Institute of Technology, School of Science and Engineering, Eugenio Garza Sada Avenue 2501 South, Monterrey, Nuevo Leon 64849, Mexico
| | - Alvaro Dario Martinez Blanco
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA; Monterrey Institute of Technology, School of Science and Engineering, Epigmenio González 500, Fraccionamiento San Pablo, Santiago de Querétaro, Querétaro 76130, Mexico
| | - Nam Ho Bae
- Center for Nano-Bio Developement, National NanoFab Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - HeaYeon Lee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA; MARA Nanotech, INC. 4th floor, Hanmir Hall, Yongdang Campus, Pukyung National University, 365 Sinseon-ro, Nam-gu, Busan 48547, Republic of Korea; MARA Nanotech New York, INC. 1 Pennsylvania Plaza, Suite 1423, New York, NY 10119, USA
| | - Su Ryon Shin
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA.
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Van De Looverbosch T, De Beuckeleer S, De Smet F, Sijbers J, De Vos WH. Proximity adjusted centroid mapping for accurate detection of nuclei in dense 3D cell systems. Comput Biol Med 2025; 185:109561. [PMID: 39693688 DOI: 10.1016/j.compbiomed.2024.109561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 11/15/2024] [Accepted: 12/08/2024] [Indexed: 12/20/2024]
Abstract
In the past decade, deep learning algorithms have surpassed the performance of many conventional image segmentation pipelines. Powerful models are now available for segmenting cells and nuclei in diverse 2D image types, but segmentation in 3D cell systems remains challenging due to the high cell density, the heterogenous resolution and contrast across the image volume, and the difficulty in generating reliable and sufficient ground truth data for model training. Reasoning that most image processing applications rely on nuclear segmentation but do not necessarily require an accurate delineation of their shapes, we implemented Proximity Adjusted Centroid MAPping (PAC-MAP), a 3D U-net based method that predicts the position of nuclear centroids and their proximity to other nuclei. We show that our model outperforms existing methods, predominantly by boosting recall, especially in conditions of high cell density. When trained from scratch with limited expert annotations (30 images), PAC-MAP attained an average F1 score of 0.793 for nuclei centroid prediction in dense spheroids. When pretraining using weakly supervised bulk data (>2300 images) followed by finetuning with the available expert annotations, the average F1 score could be significantly improved to 0.816. We demonstrate the utility of our method for quantifying the absolute cell content of spheroids and comprehensively mapping the infiltration pattern of patient-derived glioblastoma cells in cerebral organoids.
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Affiliation(s)
- Tim Van De Looverbosch
- Laboratory of Cell Biology and Histology, University of Antwerp, 2610, Antwerpen, Belgium
| | - Sarah De Beuckeleer
- Laboratory of Cell Biology and Histology, University of Antwerp, 2610, Antwerpen, Belgium
| | - Frederik De Smet
- Laboratory for Precision Cancer Medicine, KU Leuven, 3000, Leuven, Belgium
| | - Jan Sijbers
- Imec-Vision Lab, University of Antwerp, 2610, Antwerpen, Belgium
| | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, University of Antwerp, 2610, Antwerpen, Belgium; IMARK, University of Antwerp, Belgium; Antwerp Centre for Advanced Microscopy, University of Antwerp, 2610, Antwerpen, Belgium; μNeuro Research Centre of Excellence, University of Antwerp, 2610, Antwerpen, Belgium.
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Liu H, Xu H, Zhu Y, Wang Z, Hu D, Yang L, Zhu Y, Galan EA, Huang R, Peng H, Ma S. A Large Model-Derived Algorithm for Complex Organoids with Internal Morphogenesis and Digital Marker Derivation. Anal Chem 2024; 96:19258-19266. [PMID: 39445667 DOI: 10.1021/acs.analchem.4c02212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
Automated segmentation and evaluation algorithms have been demonstrated to enhance the simplicity and translational utility of organoid technology. However, there is a pressing need for the development of complex organoids that possess epithelium environmental elements, dense regional cell aggregation, and intraorganoid morphologies. Nevertheless, there has been limited progress, including both the construction of data sets and the development of algorithms, in the use of user-friendly microscopy to address such complex organoids. In this study, a data set of bright-field and living cell fluorescence images in paired forms and with temporal variance was constructed using droplet-engineered lung organoids. Additionally, a large model-based algorithm was developed. Both the organoid contours and intraorganoid morphologies were included in the data set, and their physical parameters were included and screened to form multiplex digital markers for organoid evaluation. The algorithm has been demonstrated to outperform existing methods and is therefore suitable for the evaluation of complex organoids. It is expected that the algorithm will facilitate the successful demonstration of AI in organoid evaluation and decision-making regarding their status.
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Affiliation(s)
- Hanghang Liu
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, China
| | - Haohan Xu
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, China
| | - Yu Zhu
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, China
| | - Zitian Wang
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, China
| | - Danni Hu
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, China
| | - Lingxiao Yang
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, China
| | - Yinheng Zhu
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, China
| | - Edgar A Galan
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, China
| | - Ruqi Huang
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, China
| | - Haiying Peng
- General Hospital of the Southern Theater Command of the Chinese People's Liberation Army, Guangzhou 510280, China
| | - Shaohua Ma
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, China
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing 100084, China
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Branciforti F, Salvi M, D’Agostino F, Marzola F, Cornacchia S, De Titta MO, Mastronuzzi G, Meloni I, Moschetta M, Porciani N, Sciscenti F, Spertini A, Spilla A, Zagaria I, Deloria AJ, Deng S, Haindl R, Szakacs G, Csiszar A, Liu M, Drexler W, Molinari F, Meiburger KM. Segmentation and Multi-Timepoint Tracking of 3D Cancer Organoids from Optical Coherence Tomography Images Using Deep Neural Networks. Diagnostics (Basel) 2024; 14:1217. [PMID: 38928633 PMCID: PMC11203156 DOI: 10.3390/diagnostics14121217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/29/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Recent years have ushered in a transformative era in in vitro modeling with the advent of organoids, three-dimensional structures derived from stem cells or patient tumor cells. Still, fully harnessing the potential of organoids requires advanced imaging technologies and analytical tools to quantitatively monitor organoid growth. Optical coherence tomography (OCT) is a promising imaging modality for organoid analysis due to its high-resolution, label-free, non-destructive, and real-time 3D imaging capabilities, but accurately identifying and quantifying organoids in OCT images remain challenging due to various factors. Here, we propose an automatic deep learning-based pipeline with convolutional neural networks that synergistically includes optimized preprocessing steps, the implementation of a state-of-the-art deep learning model, and ad-hoc postprocessing methods, showcasing good generalizability and tracking capabilities over an extended period of 13 days. The proposed tracking algorithm thoroughly documents organoid evolution, utilizing reference volumes, a dual branch analysis, key attribute evaluation, and probability scoring for match identification. The proposed comprehensive approach enables the accurate tracking of organoid growth and morphological changes over time, advancing organoid analysis and serving as a solid foundation for future studies for drug screening and tumor drug sensitivity detection based on organoids.
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Affiliation(s)
- Francesco Branciforti
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Massimo Salvi
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Filippo D’Agostino
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Francesco Marzola
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Sara Cornacchia
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Maria Olimpia De Titta
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Girolamo Mastronuzzi
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Isotta Meloni
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Miriam Moschetta
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Niccolò Porciani
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Fabrizio Sciscenti
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Alessandro Spertini
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Andrea Spilla
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Ilenia Zagaria
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Abigail J. Deloria
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria; (A.J.D.); (S.D.); (R.H.); (M.L.); (W.D.)
| | - Shiyu Deng
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria; (A.J.D.); (S.D.); (R.H.); (M.L.); (W.D.)
| | - Richard Haindl
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria; (A.J.D.); (S.D.); (R.H.); (M.L.); (W.D.)
| | - Gergely Szakacs
- Center for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; (G.S.); (A.C.)
| | - Agnes Csiszar
- Center for Cancer Research, Medical University of Vienna, 1090 Vienna, Austria; (G.S.); (A.C.)
| | - Mengyang Liu
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria; (A.J.D.); (S.D.); (R.H.); (M.L.); (W.D.)
| | - Wolfgang Drexler
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, 1090 Vienna, Austria; (A.J.D.); (S.D.); (R.H.); (M.L.); (W.D.)
| | - Filippo Molinari
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
| | - Kristen M. Meiburger
- Biolab, PolitoMed Lab, Department of Electronics and Telecommunications, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (F.B.); (M.S.); (F.D.); (F.M.); (S.C.); (M.O.D.T.); (G.M.); (I.M.); (M.M.); (N.P.); (F.S.); (A.S.); (A.S.); (I.Z.); (F.M.)
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