1
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Chang LY, Hao TY, Wang WJ, Lin CY. Inference of single-cell network using mutual information for scRNA-seq data analysis. BMC Bioinformatics 2024; 25:292. [PMID: 39237886 PMCID: PMC11378379 DOI: 10.1186/s12859-024-05895-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 08/08/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND With the advance in single-cell RNA sequencing (scRNA-seq) technology, deriving inherent biological system information from expression profiles at a single-cell resolution has become possible. It has been known that network modeling by estimating the associations between genes could better reveal dynamic changes in biological systems. However, accurately constructing a single-cell network (SCN) to capture the network architecture of each cell and further explore cell-to-cell heterogeneity remains challenging. RESULTS We introduce SINUM, a method for constructing the SIngle-cell Network Using Mutual information, which estimates mutual information between any two genes from scRNA-seq data to determine whether they are dependent or independent in a specific cell. Experiments on various scRNA-seq datasets with different cell numbers based on eight performance indexes (e.g., adjusted rand index and F-measure index) validated the accuracy and robustness of SINUM in cell type identification, superior to the state-of-the-art SCN inference method. Additionally, the SINUM SCNs exhibit high overlap with the human interactome and possess the scale-free property. CONCLUSIONS SINUM presents a view of biological systems at the network level to detect cell-type marker genes/gene pairs and investigate time-dependent changes in gene associations during embryo development. Codes for SINUM are freely available at https://github.com/SysMednet/SINUM .
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Affiliation(s)
- Lan-Yun Chang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan
| | - Ting-Yi Hao
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Jie Wang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chun-Yu Lin
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan.
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan.
- Institute of Data Science and Engineering, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan.
- Center for Intelligent Drug Systems and Smart Bio-Devices, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan.
- Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan.
- School of Dentistry, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
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2
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Tamagawa H, Fujii M, Togasaki K, Seino T, Kawasaki S, Takano A, Toshimitsu K, Takahashi S, Ohta Y, Matano M, Kawasaki K, Machida Y, Sekine S, Machinaga A, Sasai K, Kodama Y, Kakiuchi N, Ogawa S, Hirano T, Seno H, Kitago M, Kitagawa Y, Iwasaki E, Kanai T, Sato T. Wnt-deficient and hypoxic environment orchestrates squamous reprogramming of human pancreatic ductal adenocarcinoma. Nat Cell Biol 2024:10.1038/s41556-024-01498-5. [PMID: 39232216 DOI: 10.1038/s41556-024-01498-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/05/2024] [Indexed: 09/06/2024]
Abstract
Human pancreatic cancer is characterized by the molecular diversity encompassing native duct-like and squamous cell-like identities, but mechanisms underlying squamous transdifferentiation have remained elusive. To comprehensively capture the molecular diversity of human pancreatic cancer, we here profiled 65 patient-derived pancreatic cancer organoid lines, including six adenosquamous carcinoma lines. H3K27me3-mediated erasure of the ductal lineage specifiers and hijacking of the TP63-driven squamous-cell programme drove squamous-cell commitment, providing survival benefit in a Wnt-deficient environment and hypoxic conditions. Gene engineering of normal pancreatic duct organoids revealed that GATA6 loss and a Wnt-deficient environment, in concert with genetic or hypoxia-mediated inactivation of KDM6A, facilitate squamous reprogramming, which in turn enhances environmental fitness. EZH2 inhibition counterbalanced the epigenetic bias and curbed the growth of adenosquamous cancer organoids. Our results demonstrate how an adversarial microenvironment dictates the molecular and histological evolution of human pancreatic cancer and provide insights into the principles and significance of lineage conversion in human cancer.
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Affiliation(s)
- Hiroki Tamagawa
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Masayuki Fujii
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan.
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
| | - Kazuhiro Togasaki
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Takashi Seino
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Shintaro Kawasaki
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Ai Takano
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
| | - Kohta Toshimitsu
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Sirirat Takahashi
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
| | - Yuki Ohta
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
| | - Mami Matano
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
| | - Kenta Kawasaki
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Yujiro Machida
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Shigeki Sekine
- Division of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | | | | | - Yuzo Kodama
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomonori Hirano
- Department of Pathology and Tumor Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Minoru Kitago
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Eisuke Iwasaki
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Takanori Kanai
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan.
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan.
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3
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Guo Y, Ren C, He Y, Wu Y, Yang X. Deciphering the spatiotemporal transcriptional landscape of intestinal diseases (Review). Mol Med Rep 2024; 30:157. [PMID: 38994768 PMCID: PMC11258600 DOI: 10.3892/mmr.2024.13281] [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: 11/21/2023] [Accepted: 04/19/2024] [Indexed: 07/13/2024] Open
Abstract
The intestines are the largest barrier organ in the human body. The intestinal barrier plays a crucial role in maintaining the balance of the intestinal environment and protecting the intestines from harmful bacterial invasion. Single‑cell RNA sequencing technology allows the detection of the different cell types in the intestine in two dimensions and the exploration of cell types that have not been fully characterized. The intestinal mucosa is highly complex in structure, and its proper functioning is linked to multiple structures in the proximal‑distal intestinal and luminal‑mucosal axes. Spatial localization is at the core of the efforts to explore the interactions between the complex structures. Spatial transcriptomics (ST) is a method that allows for comprehensive tissue analysis and the acquisition of spatially separated genetic information from individual cells, while preserving their spatial location and interactions. This approach also prevents the loss of fragile cells during tissue disaggregation. The emergence of ST technology allows us to spatially dissect enzymatic processes and interactions between multiple cells, genes, proteins and signals in the intestine. This includes the exchange of oxygen and nutrients in the intestine, different gradients of microbial populations and the role of extracellular matrix proteins. This regionally precise approach to tissue studies is gaining more acceptance and is increasingly applied in the investigation of disease mechanisms related to the gastrointestinal tract. Therefore, this review summarized the application of ST in gastrointestinal diseases.
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Affiliation(s)
- Yajing Guo
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610075, P.R. China
| | - Chao Ren
- Graduate School, Hunan University of Traditional Chinese Medicine, Changsha, Hunan 410208, P.R. China
| | - Yuxi He
- Department of Digestive Medicine, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing 400021, P.R. China
| | - Yue Wu
- Department of Digestive Medicine, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing 400021, P.R. China
| | - Xiaojun Yang
- Department of Digestive Medicine, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing 400021, P.R. China
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Lekkala VKR, Shrestha S, Qaryoute AA, Dhinoja S, Acharya P, Raheem A, Jagadeeswaran P, Lee MY. Enhanced Maturity and Functionality of Vascularized Human Liver Organoids through 3D Bioprinting and Pillar Plate Culture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.608997. [PMID: 39229042 PMCID: PMC11370572 DOI: 10.1101/2024.08.21.608997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Liver tissues, composed of hepatocytes, cholangiocytes, stellate cells, Kupffer cells, and sinusoidal endothelial cells, are differentiated from endodermal and mesodermal germ layers. By mimicking the developmental process of the liver, various differentiation protocols have been published to generate human liver organoids (HLOs) in vitro using induced pluripotent stem cells (iPSCs). However, HLOs derived solely from the endodermal germ layer often encounter technical hurdles, such as insufficient maturity and functionality, limiting their utility for disease modeling and hepatotoxicity assays. To overcome this, we separately differentiated EpCAM+ endodermal progenitor cells (EPCs) and mesoderm-derived vascular progenitor cells (VPCs) from the same human iPSC line. These cells were then mixed in BME-2 matrix and concurrently differentiated into vascular human liver organoids (vHLOs). Remarkably, vHLOs exhibited significantly higher maturity than vasculature-free HLOs, as demonstrated by increased coagulation factor secretion, albumin secretion, drug-metabolizing enzyme (DME) expression, and bile acid transportation. To enhance assay throughput and miniaturize vHLO culture, we 3D bioprinted expandable HLOs (eHLOs) in BME-2 matrix on a pillar plate platform derived from EPCs and VPCs and compared with HLOs derived from endoderm alone. Compared to HLOs cultured in a 50 μL BME-2 matrix dome in a 24-well plate, vHLOs cultured on the pillar plate exhibited superior maturity, likely due to enhanced nutrient and signaling molecule diffusion. The integration of physiologically relevant patterned liver organoids with the unique pillar plate platform enhanced the capabilities for high-throughput screening and disease modeling.
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Affiliation(s)
| | - Sunil Shrestha
- Department of Biomedical Engineering, University of North Texas, Denton, Texas, USA
| | - Ayah Al Qaryoute
- Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Sanchi Dhinoja
- Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Prabha Acharya
- Department of Biomedical Engineering, University of North Texas, Denton, Texas, USA
| | - Abida Raheem
- Department of Biomedical Engineering, University of North Texas, Denton, Texas, USA
| | - Pudur Jagadeeswaran
- Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Moo-Yeal Lee
- Department of Biomedical Engineering, University of North Texas, Denton, Texas, USA
- Bioprinting Laboratories Inc., Dallas, Texas, USA
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5
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Kano M. Parathyroid Gland Generation from Pluripotent Stem Cells. Endocrinol Metab (Seoul) 2024; 39:552-558. [PMID: 38853617 PMCID: PMC11375298 DOI: 10.3803/enm.2024.1989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/07/2024] [Indexed: 06/11/2024] Open
Abstract
Patients with permanent hypoparathyroidism require lifelong treatment. Current replacement therapies sometimes have adverse effects (e.g., hypercalciuria and chronic kidney disease). Generating parathyroid glands (PTGs) from the patient's own induced pluripotent stem cells (PSCs), with transplantation of these PTGs, would be an effective treatment option. Multiple methods for generating PTGs from PSCs have been reported. One major trend is in vitro differentiation of PSCs into PTGs. Another is in vivo generation of PSC-derived PTGs by injecting PSCs into PTG-deficient embryos. This review discusses current achievements and challenges in present and future PTG regenerative medicine.
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Affiliation(s)
- Mayuko Kano
- Department of Metabolism and Endocrinology, St. Marianna University School of Medicine, Kawasaki, Japan
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6
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Ma X, Dai L, Tan C, Li J, He X, Wang Y, Xue J, Huang M, Ren J, Xia Y, Wu Q, Zhao H, Chan WY, Feng B. β-catenin mediates endodermal commitment of human ES cells via distinct transactivation functions. Cell Biosci 2024; 14:96. [PMID: 39049023 PMCID: PMC11267888 DOI: 10.1186/s13578-024-01279-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND β-catenin, acting as the core effector of canonical Wnt signaling pathway, plays a pivotal role in controlling lineage commitment and the formation of definitive endoderm (DE) during early embryonic development. Despite extensive studies using various animal and cell models, the β-catenin-centered regulatory mechanisms underlying DE formation remain incompletely understood, partly due to the rapid and complex cell fate transitions during early differentiation. RESULTS In this study, we generated new CTNNB1-/- human ES cells (hESCs) using CRISPR-based insertional gene disruption approach and systematically rescued the DE defect in these cells by introducing various truncated or mutant forms of β-catenin. Our analysis showed that a truncated β-catenin lacking both N- and C-terminal domains (ΔN148C) could robustly rescue the DE formation, whereas hyperactive β-catenin mutants with S33Y mutation or N-terminal deletion (ΔN90) had limited ability to induce DE lineage. Notably, the ΔN148C mutant exhibited significant nuclear translocation that was positively correlated with successful DE rescue. Transcriptomic analysis further uncovered that two weak β-catenin mutants lacking the C-terminal transactivation domain (CTD) activated primitive streak (PS) genes, whereas the hyperactive β-catenin mutants activated mesoderm genes. CONCLUSION Our study uncovered an unconventional regulatory function of β-catenin through weak transactivation, indicating that the levels of β-catenin activity determine the lineage bifurcation from mesendoderm into endoderm and mesoderm.
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Affiliation(s)
- Xun Ma
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
| | - Liujiang Dai
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
| | - Chunlai Tan
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jiangchuan Li
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiangjun He
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yaofeng Wang
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
| | - Junyi Xue
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Min Huang
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau SAR, China
| | - Jianwei Ren
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
| | - Yin Xia
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qiang Wu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau SAR, China
| | - Hui Zhao
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- The Chinese University of Hong Kong, Shenzhen Research Institute, Shenzhen, 518000, China
| | - Wai-Yee Chan
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- The Chinese University of Hong Kong, Shenzhen Research Institute, Shenzhen, 518000, China
| | - Bo Feng
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China.
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- The Chinese University of Hong Kong, Shenzhen Research Institute, Shenzhen, 518000, China.
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7
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Zhang X, Chen YC, Yao M, Xiong R, Liu B, Zhu X, Ao P. Potential therapeutic targets of gastric cancer explored under endogenous network modeling of clinical data. Sci Rep 2024; 14:13127. [PMID: 38849404 PMCID: PMC11161650 DOI: 10.1038/s41598-024-63812-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
Improvement in the survival rate of gastric cancer, a prevalent global malignancy and the leading cause of cancer-related mortality calls for more avenues in molecular therapy. This work aims to comprehend drug resistance and explore multiple-drug combinations for enhanced therapeutic treatment. An endogenous network modeling clinic data with core gastric cancer molecules, functional modules, and pathways is constructed, which is then transformed into dynamics equations for in-silicon studies. Principal component analysis, hierarchical clustering, and K-means clustering are utilized to map the attractor domains of the stochastic model to the normal and pathological phenotypes identified from the clinical data. The analyses demonstrate gastric cancer as a cluster of stable states emerging within the stochastic dynamics and elucidate the cause of resistance to anti-VEGF monotherapy in cancer treatment as the limitation of the single pathway in preventing cancer progression. The feasibility of multiple objectives of therapy targeting specified molecules and/or pathways is explored. This study verifies the rationality of the platform of endogenous network modeling, which contributes to the development of cross-functional multi-target combinations in clinical trials.
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Affiliation(s)
- Xile Zhang
- Center for Quantitative Life Sciences and Physics Department, Shanghai University, Shanghai, 200444, China
| | - Yong-Cong Chen
- Center for Quantitative Life Sciences and Physics Department, Shanghai University, Shanghai, 200444, China.
| | - Mengchao Yao
- Center for Quantitative Life Sciences and Physics Department, Shanghai University, Shanghai, 200444, China
| | - Ruiqi Xiong
- Center for Quantitative Life Sciences and Physics Department, Shanghai University, Shanghai, 200444, China
| | - Bingya Liu
- Department of General Surgery, Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory of Gastric Cancer, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaomei Zhu
- Shanghai Key Laboratory of Modern Optical Systems, School of Optoelectronic Information and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Ping Ao
- School of Biomedical Engineering, Sichuan University, Chengdu, 610065, China
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8
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Liu Z, Hu Y, Xie H, Chen K, Wen L, Fu W, Zhou X, Tang F. Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers. Cancer Discov 2024; 14:1082-1105. [PMID: 38445965 DOI: 10.1158/2159-8290.cd-23-1445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/06/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]
Abstract
Colorectal cancer is a highly heterogeneous disease, with well-characterized subtypes based on genome, DNA methylome, and transcriptome signatures. To chart the epigenetic landscape of colorectal cancers, we generated a high-quality single-cell chromatin accessibility atlas of epithelial cells for 29 patients. Abnormal chromatin states acquired in adenomas were largely retained in colorectal cancers, which were tightly accompanied by opposite changes of DNA methylation. Unsupervised analysis on malignant cells revealed two epigenetic subtypes, exactly matching the iCMS classification, and key iCMS-specific transcription factors (TFs) were identified, including HNF4A and PPARA for iCMS2 tumors and FOXA3 and MAFK for iCMS3 tumors. Notably, subtype-specific TFs bind to distinct target gene sets and contribute to both interpatient similarities and diversities for both chromatin accessibilities and RNA expressions. Moreover, we identified CpG-island methylator phenotypes and pinpointed chromatin state signatures and TF regulators for the CIMP-high subtype. Our work systematically revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers. SIGNIFICANCE Our work revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers. Moreover, interpatient minor similarities and major diversities of chromatin accessibility signatures of TF target genes can faithfully explain the corresponding interpatient minor similarities and major diversities of RNA expression signatures of colorectal cancers, respectively. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Zhenyu Liu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yuqiong Hu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Haoling Xie
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Kexuan Chen
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Lu Wen
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Wei Fu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Peking University Third Hospital Cancer Center, Beijing, China
| | - Xin Zhou
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Peking University Third Hospital Cancer Center, Beijing, China
| | - Fuchou Tang
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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9
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Magro-Lopez E, Vazquez-Alejo E, Espinar-Buitrago MDLS, Muñoz-Fernández MÁ. Optimizing Nodal, Wnt and BMP signaling pathways for robust and efficient differentiation of human induced pluripotent stem cells to intermediate mesoderm cells. Front Cell Dev Biol 2024; 12:1395723. [PMID: 38887514 PMCID: PMC11182123 DOI: 10.3389/fcell.2024.1395723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/06/2024] [Indexed: 06/20/2024] Open
Abstract
Several differentiation protocols have enabled the generation of intermediate mesoderm (IM)-derived cells from human pluripotent stem cells (hPSC). However, the substantial variability between existing protocols for generating IM cells compromises their efficiency, reproducibility, and overall success, potentially hindering the utility of urogenital system organoids. Here, we examined the role of high levels of Nodal signaling and BMP activity, as well as WNT signaling in the specification of IM cells derived from a UCSD167i-99-1 human induced pluripotent stem cells (hiPSC) line. We demonstrate that precise modulation of WNT and BMP signaling significantly enhances IM differentiation efficiency. Treatment of hPSC with 3 μM CHIR99021 induced TBXT+/MIXL1+ mesoderm progenitor (MP) cells after 48 h of differentiation. Further treatment with a combination of 3 μM CHIR99021 and 4 ng/mL BMP4 resulted in the generation of OSR1+/GATA3+/PAX2+ IM cells within a subsequent 48 h period. Molecular characterization of differentiated cells was confirmed through immunofluorescence staining and RT-qPCR. Hence, this study establishes a consistent and reproducible protocol for differentiating hiPSC into IM cells that faithfully recapitulates the molecular signatures of IM development. This protocol holds promise for improving the success of protocols designed to generate urogenital system organoids in vitro, with potential applications in regenerative medicine, drug discovery, and disease modeling.
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Affiliation(s)
- Esmeralda Magro-Lopez
- Molecular Immuno-Biology Laboratory, Immunology Section, Hospital General Universitario Gregorio Marañón (HGUGM), Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Elena Vazquez-Alejo
- Molecular Immuno-Biology Laboratory, Immunology Section, Hospital General Universitario Gregorio Marañón (HGUGM), Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María de la Sierra Espinar-Buitrago
- Molecular Immuno-Biology Laboratory, Immunology Section, Hospital General Universitario Gregorio Marañón (HGUGM), Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María Ángeles Muñoz-Fernández
- Molecular Immuno-Biology Laboratory, Immunology Section, Hospital General Universitario Gregorio Marañón (HGUGM), Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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10
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Parslow VR, Elmore SA, Cochran RZ, Bolon B, Mahler B, Sabio D, Lubeck BA. Histology Atlas of the Developing Mouse Respiratory System From Prenatal Day 9.0 Through Postnatal Day 30. Toxicol Pathol 2024; 52:153-227. [PMID: 39096105 DOI: 10.1177/01926233241252114] [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] [Indexed: 08/04/2024]
Abstract
Respiratory diseases are one of the leading causes of death and disability around the world. Mice are commonly used as models of human respiratory disease. Phenotypic analysis of mice with spontaneous, congenital, inherited, or treatment-related respiratory tract abnormalities requires investigators to discriminate normal anatomic features of the respiratory system from those that have been altered by disease. Many publications describe individual aspects of normal respiratory tract development, primarily focusing on morphogenesis of the trachea and lung. However, a single reference providing detailed low- and high-magnification, high-resolution images of routine hematoxylin and eosin (H&E)-stained sections depicting all major structures of the entire developing murine respiratory system does not exist. The purpose of this atlas is to correct this deficiency by establishing one concise reference of high-resolution color photomicrographs from whole-slide scans of H&E-stained tissue sections. The atlas has detailed descriptions and well-annotated images of the developing mouse upper and lower respiratory tracts emphasizing embryonic days (E) 9.0 to 18.5 and major early postnatal events. The selected images illustrate the main structures and events at key developmental stages and thus should help investigators both confirm the chronological age of mouse embryos and distinguish normal morphology as well as structural (cellular and organ) abnormalities.
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Affiliation(s)
| | - Susan A Elmore
- Experimental Pathology Laboratories, Inc., Research Triangle Park, North Carolina, USA
| | - Robert Z Cochran
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | | | - Beth Mahler
- Experimental Pathology Laboratories, Inc., Research Triangle Park, North Carolina, USA
| | - David Sabio
- Experimental Pathology Laboratories, Inc., Research Triangle Park, North Carolina, USA
| | - Beth A Lubeck
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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11
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Yang Y, Li S, Luo L. Responses of organ precursors to correct and incorrect inductive signals. Trends Cell Biol 2024; 34:484-495. [PMID: 37739814 DOI: 10.1016/j.tcb.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/24/2023]
Abstract
During embryonic development, the inductive molecules produced by local origins normally arrive at their target tissues in a nondirectional, diffusion manner. The target organ precursor cells must correctly interpret these inductive signals to ensure proper specification/differentiation, which is dependent on two prerequisites: (i) obtaining cell-intrinsic competence; and (ii) receiving correct inductive signals while resisting incorrect ones. Gain of intrinsic competence could avoid a large number of misinductions because the incompetent cells are nonresponsive to inductive signals. However, in cases of different precursor cells with similar competence and located in close proximity, resistance to incorrect inductive signals is essential for accurate determination of cell fate. Here we outline the mechanisms of how organ precursors respond to correct and incorrect inductive signals.
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Affiliation(s)
- Yun Yang
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China
| | - Shuang Li
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China
| | - Lingfei Luo
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China; School of Life Sciences, Fudan University, Shanghai, China.
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12
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Shah MA, Xie X, Rodina M, Stundl J, Braasch I, Šindelka R, Rzepkowska M, Saito T, Pšenička M. Sturgeon gut development: a unique yolk utilization strategy among vertebrates. Front Cell Dev Biol 2024; 12:1358702. [PMID: 38872929 PMCID: PMC11169612 DOI: 10.3389/fcell.2024.1358702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/08/2024] [Indexed: 06/15/2024] Open
Abstract
In vertebrates, maternally supplied yolk is typically used in one of two ways: either intracellularly by endodermal cells or extracellularly via the yolk sac. This study delves into the distinctive gut development in sturgeons, which are among the most ancient extant fish groups, contrasting it with that of other vertebrates. Our observations indicate that while sturgeon endodermal cells form the archenteron (i.e., the primitive gut) dorsally, the floor of the archenteron is uniquely composed of extraembryonic yolk cells (YCs). As development progresses, during neurulation, the archenteric cavity inflates, expands laterally, and roofs a semicircle of YCs. By the pharyngula stage, the cavity fully encompasses the YC mass, which begins to be digested at the hatching stage. This suggests a notable deviation in sturgeon gut development from that in other vertebrates, as their digestive tract initiates its function by processing endogenous nutrition even before external feeding begins. Our findings highlight the evolutionary diversity of gut development strategies among vertebrates and provide new insights into the developmental biology of sturgeons.
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Affiliation(s)
- Mujahid Ali Shah
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Vodnany, Czechia
| | - Xuan Xie
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Vodnany, Czechia
| | - Marek Rodina
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Vodnany, Czechia
| | - Jan Stundl
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Vodnany, Czechia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ingo Braasch
- Department of Integrative Biology and Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Radek Šindelka
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Małgorzata Rzepkowska
- Department of Ichthyology and Biotechnology in Aquaculture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Taiju Saito
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Vodnany, Czechia
- South Ehime Fisheries Research Centre, Ehime University, Matsuyama, Japan
| | - Martin Pšenička
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Vodnany, Czechia
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13
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Zhang C, Shan Y, Lin H, Zhang Y, Xing Q, Zhu J, Zhou T, Lin A, Chen Q, Wang J, Pan G. HBO1 determines SMAD action in pluripotency and mesendoderm specification. Nucleic Acids Res 2024; 52:4935-4949. [PMID: 38421638 PMCID: PMC11109972 DOI: 10.1093/nar/gkae158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/11/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024] Open
Abstract
TGF-β signaling family plays an essential role to regulate fate decisions in pluripotency and lineage specification. How the action of TGF-β family signaling is intrinsically executed remains not fully elucidated. Here, we show that HBO1, a MYST histone acetyltransferase (HAT) is an essential cell intrinsic determinant for TGF-β signaling in human embryonic stem cells (hESCs). HBO1-/- hESCs fail to response to TGF-β signaling to maintain pluripotency and spontaneously differentiate into neuroectoderm. Moreover, HBO1 deficient hESCs show complete defect in mesendoderm specification in BMP4-triggered gastruloids or teratomas. Molecularly, HBO1 interacts with SMAD4 and co-binds the open chromatin labeled by H3K14ac and H3K4me3 in undifferentiated hESCs. Upon differentiation, HBO1/SMAD4 co-bind and maintain the mesoderm genes in BMP4-triggered mesoderm cells while lose chromatin occupancy in neural cells induced by dual-SMAD inhibition. Our data reveal an essential role of HBO1, a chromatin factor to determine the action of SMAD in both human pluripotency and mesendoderm specification.
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Affiliation(s)
- Cong Zhang
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Yongli Shan
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Huaisong Lin
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Yanqi Zhang
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Qi Xing
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Jinmin Zhu
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Tiancheng Zhou
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Aiping Lin
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Qianyu Chen
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Junwei Wang
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
| | - Guangjin Pan
- Key Laboratory of Immune Response and Immunotherapy, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530,China; Guangzhou Medical University, Guangzhou 511436, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Center for Cell Lineage and Cell Therapy, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, China
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14
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Sanchez JG, Rankin S, Paul E, McCauley HA, Kechele DO, Enriquez JR, Jones NH, Greeley SAW, Letourneau-Friedberg L, Zorn AM, Krishnamurthy M, Wells JM. RFX6 regulates human intestinal patterning and function upstream of PDX1. Development 2024; 151:dev202529. [PMID: 38587174 PMCID: PMC11128285 DOI: 10.1242/dev.202529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/12/2024] [Indexed: 04/09/2024]
Abstract
The gastrointestinal (GI) tract is complex and consists of multiple organs with unique functions. Rare gene variants can cause congenital malformations of the human GI tract, although the molecular basis of these has been poorly studied. We identified a patient with compound-heterozygous variants in RFX6 presenting with duodenal malrotation and atresia, implicating RFX6 in development of the proximal intestine. To identify how mutations in RFX6 impact intestinal patterning and function, we derived induced pluripotent stem cells from this patient to generate human intestinal organoids (HIOs). We identified that the duodenal HIOs and human tissues had mixed regional identity, with gastric and ileal features. CRISPR-mediated correction of RFX6 restored duodenal identity. We then used gain- and loss-of-function and transcriptomic approaches in HIOs and Xenopus embryos to identify that PDX1 is a downstream transcriptional target of RFX6 required for duodenal development. However, RFX6 had additional PDX1-independent transcriptional targets involving multiple components of signaling pathways that are required for establishing early regional identity in the GI tract. In summary, we have identified RFX6 as a key regulator in intestinal patterning that acts by regulating transcriptional and signaling pathways.
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Affiliation(s)
- J. Guillermo Sanchez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Scott Rankin
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Emily Paul
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Heather A. McCauley
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Daniel O. Kechele
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Jacob R. Enriquez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Nana-Hawa Jones
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Siri A. W. Greeley
- Division of Endocrinology, University of Chicago, Chicago, IL 60637, USA
| | | | - Aaron M. Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
| | - Mansa Krishnamurthy
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - James M. Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229, USA
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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15
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Zheng C, Wang J, Wang J, Zhang Q, Liang T. Cell of Origin of Pancreatic cancer: Novel Findings and Current Understanding. Pancreas 2024; 53:e288-e297. [PMID: 38277420 DOI: 10.1097/mpa.0000000000002301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
ABSTRACT Pancreatic ductal adenocarcinoma (PDAC) stands as one of the most lethal diseases globally, boasting a grim 5-year survival prognosis. The origin cell and the molecular signaling pathways that drive PDAC progression are not entirely understood. This review comprehensively outlines the categorization of PDAC and its precursor lesions, expounds on the creation and utility of genetically engineered mouse models used in PDAC research, compiles a roster of commonly used markers for pancreatic progenitors, duct cells, and acinar cells, and briefly addresses the mechanisms involved in the progression of PDAC. We acknowledge the value of precise markers and suitable tracing tools to discern the cell of origin, as it can facilitate the creation of more effective models for PDAC exploration. These conclusions shed light on our existing understanding of foundational genetically engineered mouse models and focus on the origin and development of PDAC.
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16
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Adkins-Threats M, Huang YZ, Mills JC. Highlights of how single-cell analyses are illuminating differentiation and disease in the gastric corpus. Am J Physiol Gastrointest Liver Physiol 2024; 326:G205-G215. [PMID: 38193187 PMCID: PMC11211037 DOI: 10.1152/ajpgi.00164.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/18/2023] [Accepted: 12/23/2023] [Indexed: 01/10/2024]
Abstract
Single-cell RNA-sequencing (scRNA-seq) has emerged as a powerful technique to identify novel cell markers, developmental trajectories, and transcriptional changes during cell differentiation and disease onset and progression. In this review, we highlight recent scRNA-seq studies of the gastric corpus in both human and murine systems that have provided insight into gastric organogenesis, identified novel markers for the various gastric lineages during development and in adults, and revealed transcriptional changes during regeneration and tumorigenesis. Overall, by elucidating transcriptional states and fluctuations at the cellular level in healthy and disease contexts, scRNA-seq may lead to better, more personalized clinical treatments for disease progression.
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Affiliation(s)
- Mahliyah Adkins-Threats
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States
| | - Yang-Zhe Huang
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States
- Graduate School of Biomedical Sciences, Cancer and Cell Biology Program, Baylor College of Medicine, Houston, Texas, United States
| | - Jason C Mills
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States
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17
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Teague S, Primavera G, Chen B, Liu ZY, Yao L, Freeburne E, Khan H, Jo K, Johnson C, Heemskerk I. Time-integrated BMP signaling determines fate in a stem cell model for early human development. Nat Commun 2024; 15:1471. [PMID: 38368368 PMCID: PMC10874454 DOI: 10.1038/s41467-024-45719-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 02/02/2024] [Indexed: 02/19/2024] Open
Abstract
How paracrine signals are interpreted to yield multiple cell fate decisions in a dynamic context during human development in vivo and in vitro remains poorly understood. Here we report an automated tracking method to follow signaling histories linked to cell fate in large numbers of human pluripotent stem cells (hPSCs). Using an unbiased statistical approach, we discover that measured BMP signaling history correlates strongly with fate in individual cells. We find that BMP response in hPSCs varies more strongly in the duration of signaling than the level. However, both the level and duration of signaling activity control cell fate choices only by changing the time integral. Therefore, signaling duration and level are interchangeable in this context. In a stem cell model for patterning of the human embryo, we show that signaling histories predict the fate pattern and that the integral model correctly predicts changes in cell fate domains when signaling is perturbed. Our data suggest that mechanistically, BMP signaling is integrated by SOX2.
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Affiliation(s)
- Seth Teague
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Gillian Primavera
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Bohan Chen
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Zong-Yuan Liu
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - LiAng Yao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Emily Freeburne
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Hina Khan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kyoung Jo
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Craig Johnson
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Idse Heemskerk
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Center for Cell Plasticity and Organ Design, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Physics, University of Michigan, Ann Arbor, MI, USA.
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18
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Miao Y, Tan C, Pek NM, Yu Z, Iwasawa K, Kechele DO, Sundaram N, Pastrana-Gomez V, Kishimoto K, Yang MC, Jiang C, Tchieu J, Whitsett JA, McCracken KW, Rottier RJ, Kotton DN, Helmrath MA, Wells JM, Takebe T, Zorn AM, Chen YW, Guo M, Gu M. Deciphering Endothelial and Mesenchymal Organ Specification in Vascularized Lung and Intestinal Organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.577460. [PMID: 38370768 PMCID: PMC10871227 DOI: 10.1101/2024.02.06.577460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
To investigate the co-development of vasculature, mesenchyme, and epithelium crucial for organogenesis and the acquisition of organ-specific characteristics, we constructed a human pluripotent stem cell-derived organoid system comprising lung or intestinal epithelium surrounded by organotypic mesenchyme and vasculature. We demonstrated the pivotal role of co-differentiating mesoderm and endoderm via precise BMP regulation in generating multilineage organoids and gut tube patterning. Single-cell RNA-seq analysis revealed organ specificity in endothelium and mesenchyme, and uncovered key ligands driving endothelial specification in the lung (e.g., WNT2B and Semaphorins) or intestine (e.g., GDF15). Upon transplantation under the kidney capsule in mice, these organoids further matured and developed perfusable human-specific sub-epithelial capillaries. Additionally, our model recapitulated the abnormal endothelial-epithelial crosstalk in patients with FOXF1 deletion or mutations. Multilineage organoids provide a unique platform to study developmental cues guiding endothelial and mesenchymal cell fate determination, and investigate intricate cell-cell communications in human organogenesis and disease. Highlights BMP signaling fine-tunes the co-differentiation of mesoderm and endoderm.The cellular composition in multilineage organoids resembles that of human fetal organs.Mesenchyme and endothelium co-developed within the organoids adopt organ-specific characteristics.Multilineage organoids recapitulate abnormal endothelial-epithelial crosstalk in FOXF1-associated disorders.
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19
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Zwick RK, Kasparek P, Palikuqi B, Viragova S, Weichselbaum L, McGinnis CS, McKinley KL, Rathnayake A, Vaka D, Nguyen V, Trentesaux C, Reyes E, Gupta AR, Gartner ZJ, Locksley RM, Gardner JM, Itzkovitz S, Boffelli D, Klein OD. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains. Nat Cell Biol 2024; 26:250-262. [PMID: 38321203 DOI: 10.1038/s41556-023-01337-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 12/13/2023] [Indexed: 02/08/2024]
Abstract
A key aspect of nutrient absorption is the exquisite division of labour across the length of the small intestine, with individual nutrients taken up at different proximal:distal positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum and ileum. By examining the fine-scale longitudinal transcriptional patterns that span the mouse and human small intestine, we instead identified five domains of nutrient absorption that mount distinct responses to dietary changes, and three regional stem cell populations. Molecular domain identity can be detected with machine learning, which provides a systematic method to computationally identify intestinal domains in mice. We generated a predictive model of transcriptional control of domain identity and validated the roles of Ppar-δ and Cdx1 in patterning lipid metabolism-associated genes. These findings represent a foundational framework for the zonation of absorption across the mammalian small intestine.
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Affiliation(s)
- Rachel K Zwick
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Petr Kasparek
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Brisa Palikuqi
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sara Viragova
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Laura Weichselbaum
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Kara L McKinley
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Asoka Rathnayake
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Dedeepya Vaka
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA
| | - Vinh Nguyen
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA
| | - Coralie Trentesaux
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Efren Reyes
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Alexander R Gupta
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
- Chan Zuckerberg BioHub and Center for Cellular Construction 94158, University of California San Francisco, San Francisco, CA, USA
| | - Richard M Locksley
- Department of Medicine and Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - James M Gardner
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dario Boffelli
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA
| | - Ophir D Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA.
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20
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Xiao YY, Zhang Q, Huang F, Rao L, Yao TX, Yang SY, Xie L, Zou XX, Cai LP, Yang JW, Yang B, Huang LS. Single-cell profiling of the pig cecum at various developmental stages. Zool Res 2024; 45:55-68. [PMID: 38114433 PMCID: PMC10839672 DOI: 10.24272/j.issn.2095-8137.2023.007] [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: 03/16/2023] [Accepted: 09/12/2023] [Indexed: 12/21/2023] Open
Abstract
The gastrointestinal tract is essential for food digestion, nutrient absorption, waste elimination, and microbial defense. Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity, functional heterogeneity, and their importance in intestinal tract development and disease. Although such profiling has been extensively conducted in humans and mice, the single-cell gene expression landscape of the pig cecum remains unexplored. Here, single-cell RNA sequencing was performed on 45 572 cells obtained from seven cecal samples in pigs at four different developmental stages (days (D) 30, 42, 150, and 730). Analysis revealed 12 major cell types and 38 subtypes, as well as their distinctive genes, transcription factors, and regulons, many of which were conserved in humans. An increase in the relative proportions of CD8 + T and Granzyme A (low expression) natural killer T cells (GZMA low NKT) cells and a decrease in the relative proportions of epithelial stem cells, Tregs, RHEX + T cells, and plasmacytoid dendritic cells (pDCs) were noted across the developmental stages. Moreover, the post-weaning period exhibited an up-regulation in mitochondrial genes, COX2 and ND2, as well as genes involved in immune activation in multiple cell types. Cell-cell crosstalk analysis indicated that IBP6 + fibroblasts were the main signal senders at D30, whereas IBP6 - fibroblasts assumed this role at the other stages. NKT cells established interactions with epithelial cells and IBP6 + fibroblasts in the D730 cecum through mediation of GZMA-F2RL1/F2RL2 pairs. This study provides valuable insights into cellular heterogeneity and function in the pig cecum at different development stages.
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Affiliation(s)
- Yan-Yuan Xiao
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Qing Zhang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Fei Huang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Lin Rao
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Tian-Xiong Yao
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Si-Yu Yang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Lei Xie
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Xiao-Xiao Zou
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Li-Ping Cai
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Jia-Wen Yang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Bin Yang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China. E-mail:
| | - Lu-Sheng Huang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China. E-mail:
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21
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Peng D, Jackson D, Palicha B, Kernfeld E, Laughner N, Shoemaker A, Celniker SE, Loganathan R, Cahan P, Andrew DJ. Organogenetic transcriptomes of the Drosophila embryo at single cell resolution. Development 2024; 151:dev202097. [PMID: 38174902 PMCID: PMC10820837 DOI: 10.1242/dev.202097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
To gain insight into the transcription programs activated during the formation of Drosophila larval structures, we carried out single cell RNA sequencing during two periods of Drosophila embryogenesis: stages 10-12, when most organs are first specified and initiate morphological and physiological specialization; and stages 13-16, when organs achieve their final mature architectures and begin to function. Our data confirm previous findings with regards to functional specialization of some organs - the salivary gland and trachea - and clarify the embryonic functions of another - the plasmatocytes. We also identify two early developmental trajectories in germ cells and uncover a potential role for proteolysis during germline stem cell specialization. We identify the likely cell type of origin for key components of the Drosophila matrisome and several commonly used Drosophila embryonic cell culture lines. Finally, we compare our findings with other recent related studies and with other modalities for identifying tissue-specific gene expression patterns. These data provide a useful community resource for identifying many new players in tissue-specific morphogenesis and functional specialization of developing organs.
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Affiliation(s)
- Da Peng
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dorian Jackson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bianca Palicha
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric Kernfeld
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nathaniel Laughner
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ashleigh Shoemaker
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Susan E. Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rajprasad Loganathan
- Department of Biological Sciences, Wichita State University, Wichita, KS 67260, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Deborah J. Andrew
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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22
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Jung JH, Yang SR, Kim WJ, Rhee CK, Hong SH. Human Pluripotent Stem Cell-Derived Alveolar Organoids: Cellular Heterogeneity and Maturity. Tuberc Respir Dis (Seoul) 2024; 87:52-64. [PMID: 37993994 PMCID: PMC10758311 DOI: 10.4046/trd.2023.0131] [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: 08/25/2023] [Revised: 11/07/2023] [Accepted: 11/22/2023] [Indexed: 11/24/2023] Open
Abstract
Chronic respiratory diseases such as idiopathic pulmonary fibrosis, chronic obstructive pulmonary disease, and respiratory infections injure the alveoli; the damage evoked is mostly irreversible and occasionally leads to death. Achieving a detailed understanding of the pathogenesis of these fatal respiratory diseases has been hampered by limited access to human alveolar tissue and the differences between mice and humans. Thus, the development of human alveolar organoid (AO) models that mimic in vivo physiology and pathophysiology has gained tremendous attention over the last decade. In recent years, human pluripotent stem cells (hPSCs) have been successfully employed to generate several types of organoids representing different respiratory compartments, including alveolar regions. However, despite continued advances in three-dimensional culture techniques and single-cell genomics, there is still a profound need to improve the cellular heterogeneity and maturity of AOs to recapitulate the key histological and functional features of in vivo alveolar tissue. In particular, the incorporation of immune cells such as macrophages into hPSC-AO systems is crucial for disease modeling and subsequent drug screening. In this review, we summarize current methods for differentiating alveolar epithelial cells from hPSCs followed by AO generation and their applications in disease modeling, drug testing, and toxicity evaluation. In addition, we review how current hPSC-AOs closely resemble in vivo alveoli in terms of phenotype, cellular heterogeneity, and maturity.
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Affiliation(s)
- Ji-hye Jung
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Republic of Korea
| | - Se-Ran Yang
- Department of Thoracic and Cardiovascular Surgery, Kangwon National University School of Medicine, Chuncheon, Republic of Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Republic of Korea
| | - Chin Kook Rhee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Republic of Korea
- KW-Bio Co., Ltd., Chuncheon, Republic of Korea
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23
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Sepyani S, Momenzadeh S, Safabakhsh S, Nedaeinia R, Salehi R. Therapeutic approaches for Type 1 Diabetes: Promising cell-based approaches to achieve ultimate success. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:23-33. [PMID: 37977308 DOI: 10.1016/j.slasd.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/12/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Type 1 Diabetes mellitus (T1DM) is a chronic metabolic disorder characterized by pancreatic β-cells destruction. Despite substantial advances in T1DM treatment, lifelong exogenous insulin administration is the mainstay of treatments, and constant control of glucose levels is still a challenge. Endogenous insulin production by replacing insulin-producing cells is an alternative, but the lack of suitable donors is accounted as one of the main obstacles to its widespread application. The research and trials overview demonstrates that endogenous production of insulin has started to go beyond the deceased-derived to stem cells-derived insulin-producing cells. Several protocols have been developed over the past couple of years for generating insulin-producing cells (IPCs) from various stem cell types and reprogramming fully differentiated cells. A straightforward and quick method for achieving this goal is to investigate and apply the β-cell specific transcription factors as a direct strategy for IPCs generation. In this review, we emphasize the significance of transcription factors in IPCs development from different non-beta cell sources, and pertinent research underlies the marked progress in the methods for generating insulin-producing cells and application for Type 1 Diabetes treatment.
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Affiliation(s)
- Sahar Sepyani
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sedigheh Momenzadeh
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Saied Safabakhsh
- Micronesian Institute for Disease Prevention and Research, 736 Route 4, Suite 103, Sinajana, GU 96910, United States
| | - Reza Nedaeinia
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rasoul Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran.
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24
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Jin Q, Hu Y, Gao Y, Zheng J, Chen J, Gao C, Peng J. Hhex and Prox1a synergistically dictate the hepatoblast to hepatocyte differentiation in zebrafish. Biochem Biophys Res Commun 2023; 686:149182. [PMID: 37922575 DOI: 10.1016/j.bbrc.2023.149182] [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: 10/18/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
The specification of endoderm cells to prospective hepatoblasts is the starting point for hepatogenesis. However, how a prospective hepatoblast gains the hepatic fate remains elusive. Previous studies have shown that loss-of-function of either hhex or prox1a alone causes a small liver phenotype but without abolishing the hepatocyte differentiation, suggesting that absence of either Hhex or Prox1a alone is not sufficient to block the hepatoblast differentiation. Here, via genetic studies of the zebrafish two single (hhex-/- and prox1a-/-) and one double (hhex-/-prox1a-/-) mutants, we show that simultaneous loss-of-function of the hhex and prox1a two genes does not block the endoderm cells to gain the hepatoblast potency but abolishes the hepatic differentiation from the prospective hepatoblast. Consequently, the hhex-/-prox1a-/- double mutant displays a liverless phenotype that cannot be rescued by the injection of bmp2a mRNA. Taken together, we provide strong evidences showing that Hhex teams with Prox1a to act as a master control of the differentiation of the prospective hepatoblasts towards hepatocytes.
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Affiliation(s)
- Qingxia Jin
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yuqing Hu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yuqi Gao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Jiayi Zheng
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Ce Gao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China.
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China.
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25
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Crow KD, Sadakian A, Kaslly NA. The role of the 5' HoxA genes in the development of the hindgut, vent, and a novel sphincter in a derived teleost (bluebanded goby, Lythrypnus dalli). JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:518-530. [PMID: 32779333 DOI: 10.1002/jez.b.22982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/05/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Unique expression patterns of the 5' HoxA genes are associated with the evolution and development of novel features including claspers in cartilaginous fishes, modified pectoral fins in batoids, and the yolk sac extension in Cypriniformes. Here, we demonstrate a role for HoxA11a and HoxA13a in demarcating the hindgut in fishes of the family Gobiidae, including a novel sphincter called the intestinal rectal sphincter (IRS). Disruption of 5' HoxA expression, via manipulation of retinoic acid signaling, results in failure of the IRS and/or vent to develop. Furthermore, exposure to HoxA disruptors alters 5' HoxA expression, in association with developmental phenotypes, demonstrating a functional link between 5' HoxA expression and development of a novel feature in the bluebanded goby, Lythrypnus dalli.
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Affiliation(s)
- Karen D Crow
- Department of Biology, San Francisco State University, San Francisco, California
| | - Ara Sadakian
- Department of Biology, San Francisco State University, San Francisco, California
| | - Noelle A Kaslly
- Department of Biology, San Francisco State University, San Francisco, California
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26
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Richardson L, Wilcockson SG, Guglielmi L, Hill CS. Context-dependent TGFβ family signalling in cell fate regulation. Nat Rev Mol Cell Biol 2023; 24:876-894. [PMID: 37596501 DOI: 10.1038/s41580-023-00638-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 08/20/2023]
Abstract
The transforming growth factor-β (TGFβ) family are a large group of evolutionarily conserved cytokines whose signalling modulates cell fate decision-making across varying cellular contexts at different stages of life. Here we discuss new findings in early embryos that reveal how, in contrast to our original understanding of morphogen interpretation, robust cell fate specification can originate from a noisy combination of signalling inputs and a broad range of signalling levels. We compare this evidence with novel findings on the roles of TGFβ family signalling in tissue maintenance and homeostasis during juvenile and adult life, spanning the skeletal, haemopoietic and immune systems. From these comparisons, it emerges that in contrast to robust developing systems, relatively small perturbations in TGFβ family signalling have detrimental effects at later stages in life, leading to aberrant cell fate specification and disease, for example in cancer or congenital disorders. Finally, we highlight novel strategies to target and amend dysfunction in signalling and discuss how gleaning knowledge from different fields of biology can help in the development of therapeutics for aberrant TGFβ family signalling in disease.
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Affiliation(s)
- Louise Richardson
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK
| | - Scott G Wilcockson
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK
| | - Luca Guglielmi
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK.
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27
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Bora J, Dey A, Lyngdoh AR, Dhasmana A, Ranjan A, Kishore S, Rustagi S, Tuli HS, Chauhan A, Rath P, Malik S. A critical review on therapeutic approaches of CRISPR-Cas9 in diabetes mellitus. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2023; 396:3459-3481. [PMID: 37522916 DOI: 10.1007/s00210-023-02631-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023]
Abstract
Diabetes mellitus (D.M.) is a common metabolic disorder caused mainly by combining two primary factors, which are (1) defects in insulin production by the pancreatic β-cells and (2) responsiveness of insulin-sensitive tissues towards insulin. Despite the rapid advancement in medicine to suppress elevated blood glucose levels (hyperglycemia) and insulin resistance associated with this hazard, a demand has undoubtedly emerged to find more effective and curative dimensions in therapeutic approaches against D.M. The administration of diabetes treatment that emphasizes insulin production and sensitivity may result in unfavorable side effects, reduced adherence, and potential treatment ineffectiveness. Recent progressions in genome editing technologies, for instance, in zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeat (CRISPR-Cas)-associated nucleases, have greatly influenced the gene editing technology from concepts to clinical practices. Improvements in genome editing technologies have also opened up the possibility to target and modify specific genome sequences in a cell directly. CRISPR/Cas9 has proven effective in utilizing ex vivo gene editing in embryonic stem cells and stem cells derived from patients. This application has facilitated the exploration of pancreatic beta-cell development and function. Furthermore, CRISPR/Cas9 enables the creation of innovative animal models for diabetes and assesses the effectiveness of different therapeutic strategies in treating the condition. We, therefore, present a critical review of the therapeutic approaches of the genome editing tool CRISPR-Cas9 in treating D.M., discussing the challenges and limitations of implementing this technology.
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Affiliation(s)
- Jutishna Bora
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, 834001, India
| | - Ankita Dey
- Department of Biochemistry, North Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Antonia R Lyngdoh
- Department of Biochemistry, North Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Archna Dhasmana
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Stachki 194/1, Rostov-On-Don, 344090, Russia
| | - Shristi Kishore
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, 834001, India
| | - Sarvesh Rustagi
- School of Applied and Life Sciences, Uttaranchal University, 22 Dehradun, Uttarakhand, India
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (Deemed to Be University), Mullana-Ambala, 133207, India
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Sector 125, Noida, Uttar Pradesh, India
| | - Prangya Rath
- Amity Institute of Environmental Sciences, Amity University, Noida, Uttar Pradesh, 201303, India
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, 834001, India.
- School of Applied and Life Sciences, Uttaranchal University, 22 Dehradun, Uttarakhand, India.
- Guru Nanak College of Pharmaceutical Sciences, Dehradun, Uttarakhand, India.
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Roberto de Barros N, Wang C, Maity S, Peirsman A, Nasiri R, Herland A, Ermis M, Kawakita S, Gregatti Carvalho B, Hosseinzadeh Kouchehbaghi N, Donizetti Herculano R, Tirpáková Z, Mohammad Hossein Dabiri S, Lucas Tanaka J, Falcone N, Choroomi A, Chen R, Huang S, Zisblatt E, Huang Y, Rashad A, Khorsandi D, Gangrade A, Voskanian L, Zhu Y, Li B, Akbari M, Lee J, Remzi Dokmeci M, Kim HJ, Khademhosseini A. Engineered organoids for biomedical applications. Adv Drug Deliv Rev 2023; 203:115142. [PMID: 37967768 PMCID: PMC10842104 DOI: 10.1016/j.addr.2023.115142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/03/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
As miniaturized and simplified stem cell-derived 3D organ-like structures, organoids are rapidly emerging as powerful tools for biomedical applications. With their potential for personalized therapeutic interventions and high-throughput drug screening, organoids have gained significant attention recently. In this review, we discuss the latest developments in engineering organoids and using materials engineering, biochemical modifications, and advanced manufacturing technologies to improve organoid culture and replicate vital anatomical structures and functions of human tissues. We then explore the diverse biomedical applications of organoids, including drug development and disease modeling, and highlight the tools and analytical techniques used to investigate organoids and their microenvironments. We also examine the latest clinical trials and patents related to organoids that show promise for future clinical translation. Finally, we discuss the challenges and future perspectives of using organoids to advance biomedical research and potentially transform personalized medicine.
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Affiliation(s)
| | - Canran Wang
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Surjendu Maity
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Arne Peirsman
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Plastic and Reconstructive Surgery, Ghent University Hospital, Ghent, Belgium
| | - Rohollah Nasiri
- Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, KTH Royal Institute of Technology, 17165 Solna, Sweden
| | - Anna Herland
- Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, KTH Royal Institute of Technology, 17165 Solna, Sweden
| | - Menekse Ermis
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Satoru Kawakita
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Bruna Gregatti Carvalho
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Department of Material and Bioprocess Engineering, School of Chemical Engineering, University of Campinas (UNICAMP), 13083-970 Campinas, Brazil
| | - Negar Hosseinzadeh Kouchehbaghi
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Department of Textile Engineering, Amirkabir University of Technology (Tehran Polytechnic), Hafez Avenue, 1591634311 Tehran, Iran
| | - Rondinelli Donizetti Herculano
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Autonomy Research Center for STEAHM (ARCS), California State University, Northridge, CA 91324, USA; São Paulo State University (UNESP), Bioengineering and Biomaterials Group, School of Pharmaceutical Sciences, Araraquara, SP, Brazil
| | - Zuzana Tirpáková
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 04181 Kosice, Slovakia
| | - Seyed Mohammad Hossein Dabiri
- Laboratory for Innovations in Micro Engineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Jean Lucas Tanaka
- Butantan Institute, Viral Biotechnology Laboratory, São Paulo, SP Brazil; University of São Paulo (USP), São Paulo, SP Brazil
| | - Natashya Falcone
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Auveen Choroomi
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - RunRun Chen
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Autonomy Research Center for STEAHM (ARCS), California State University, Northridge, CA 91324, USA
| | - Shuyi Huang
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Autonomy Research Center for STEAHM (ARCS), California State University, Northridge, CA 91324, USA
| | - Elisheva Zisblatt
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Yixuan Huang
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Ahmad Rashad
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Danial Khorsandi
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Ankit Gangrade
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Leon Voskanian
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Yangzhi Zhu
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA
| | - Bingbing Li
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; Autonomy Research Center for STEAHM (ARCS), California State University, Northridge, CA 91324, USA
| | - Mohsen Akbari
- Laboratory for Innovations in Micro Engineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Junmin Lee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, Republic of Korea
| | | | - Han-Jun Kim
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA; College of Pharmacy, Korea University, Sejong 30019, Republic of Korea.
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA 90064, USA.
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Oikonomou P, Cirne HC, Nerurkar NL. A chemo-mechanical model of endoderm movements driving elongation of the amniote hindgut. Development 2023; 150:dev202010. [PMID: 37840469 PMCID: PMC10690059 DOI: 10.1242/dev.202010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
Although mechanical and biochemical descriptions of development are each essential, integration of upstream morphogenic cues with downstream tissue mechanics remains understudied during vertebrate morphogenesis. Here, we developed a two-dimensional chemo-mechanical model to investigate how mechanical properties of the endoderm and transport properties of fibroblast growth factor (FGF) regulate avian hindgut morphogenesis in a coordinated manner. Posterior endoderm cells convert a gradient of FGF ligands into a contractile force gradient, leading to a force imbalance that drives collective cell movements that elongate the forming hindgut tube. We formulated a 2D reaction-diffusion-advection model describing the formation of an FGF protein gradient as a result of posterior displacement of cells transcribing unstable Fgf8 mRNA during axis elongation, coupled with translation, diffusion and degradation of FGF protein. The endoderm was modeled as an active viscous fluid that generates contractile stresses in proportion to FGF concentration. With parameter values constrained by experimental data, the model replicates key aspects of hindgut morphogenesis, suggests that graded isotropic contraction is sufficient to generate large anisotropic cell movements, and provides new insight into how chemo-mechanical coupling across the mesoderm and endoderm coordinates hindgut elongation with axis elongation.
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Affiliation(s)
- Panagiotis Oikonomou
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Helena C. Cirne
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Nandan L. Nerurkar
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
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30
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Iguchi R, Nakayama S, Sasakura Y, Sekiguchi T, Ogasawara M. Repetitive and zonal expression profiles of absorption-related genes in the gastrointestinal tract of ascidian Ciona intestinalis type A. Cell Tissue Res 2023; 394:343-360. [PMID: 37670165 DOI: 10.1007/s00441-023-03828-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/15/2023] [Indexed: 09/07/2023]
Abstract
Intestinal absorption is essential for heterotrophic bilaterians with a tubular gut. Although the fundamental features of the digestive system were shared among chordates with evolution, the gut morphologies of vertebrates diverged and adapted to different food habitats. The ascidian Ciona intestinalis type A, a genome-wide research model of basal chordates, is used to examine the functional morphology of the intestines because of its transparent juvenile body. In the present study, the characteristic gene expression patterns (GEP) of Ciona absorptive proteins, e.g., brush border membrane enzymes for terminal digestion (lactase, maltase, APA, and APN) and transporters (SGLT1, GLUT5, PEPT1, and B0AT1), were investigated in juveniles and young adults, with a special reference to the absorption of other nutrients by pinocytosis- and phagocytosis-related proteins (megalin, cubilin, amnionless, Dab2, Rab7, LAMP, cathepsins, and MRC1). Whole-mount in situ hybridization revealed that these GEP showed multi-regional and repetitive features along the Ciona gastrointestinal tract, mainly in the stomach and several regions of the intestines. In young adults, many absorption-related genes, including pinocytosis-/phagocytosis-related genes, were also expressed between the stomach and mid-intestine. In the gastrointestinal epithelium, absorption-related genes showed zonal GEP along the epithelial structure. Comparisons of GEP, including other intestinal functions, such as nutrient digestion and intestinal protection, indicated the repetitive assignment of a well-coordinated set of intestinal GEP in the Ciona gastrointestinal tract.
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Affiliation(s)
- Rin Iguchi
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage-Ku, Chiba, 263-8522, Japan
| | - Satoshi Nakayama
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage-Ku, Chiba, 263-8522, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Toshio Sekiguchi
- The Noto Marine Laboratory, Division of Marine Environmental Studies, Institute of Nature and Environmental Technology, Kanazawa University, Housu-Gun, Ishikawa, 927-0553, Japan
| | - Michio Ogasawara
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage-Ku, Chiba, 263-8522, Japan.
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31
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da Silva Nunes Barreto R, da Silva Júnior LN, Henrique Doná Rodrigues Almeida G, de Oliveira Horvath-Pereira B, da Silva TS, Garcia JM, Smith LC, Carreira ACO, Miglino MA. Placental scaffolds as a potential biological platform for embryonic stem cells differentiation into hepatic-like cells lineage: A pilot study. Tissue Cell 2023; 84:102181. [PMID: 37515966 DOI: 10.1016/j.tice.2023.102181] [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: 05/21/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 07/31/2023]
Abstract
Hepatic microenvironment plays an essential role in liver regeneration, providing the necessary conditions for cell proliferation, differentiation and tissue rearrangement. One of the key factors for hepatic tissue reconstruction is the extracellular matrix (ECM), which through collagenous and non-collagenous proteins provide a three-dimensional structure that confers support for cell adhesion and assists on their survival and maintenance. In this scenario, placental ECM may be eligible for hepatic tissue reconstruction, once these scaffolds hold the major components required for cell support. Therefore, this preliminary study aimed to access the possibility of mouse embryonic stem cells differentiation into hepatocyte-like cells on placental scaffolds in a three-dimensional dynamic system using a Rotary Cell Culture System. Following a four-phase differentiation protocol that simulates liver embryonic development events, the preliminary results showed that a significant quantity of cells adhered and interacted with the scaffold through outer and inner surfaces. Positive immunolabelling for alpha fetus protein and CK7 suggest presence of hepatoblast phenotype cells, and CK18 and Albumin positive immunolabelling suggest the presence of hepatocyte-like phenotype cells, demonstrating the presence of a heterogeneous population into the recellularized scaffolds. Periodic Acid Schiff-Diastase staining confirmed the presence of glycogen storage, indicating that differentiate cells acquired a hepatic-like phenotype. In conclusion, these preliminary results suggested that mouse placental scaffolds might be used as a biological platform for stem cells differentiation into hepatic-like cells and their establishment, which may be a promissing biomaterial for hepatic tissue reconstruction.
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Affiliation(s)
| | | | | | | | - Thamires Santos da Silva
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, SP, Brazil
| | - Joaquim Mansano Garcia
- Department of Preventive Veterinary Medicine and Animal Reproduction, Faculty of Agricultural and Veterinary Sciences, State University of São Paulo, Jaboticabal, SP, Brazil
| | - Lawrence Charles Smith
- Centre de Recherche en Reproduction et Fertilité, University of Montreal, Montreal, QC, Canada
| | - Ana Claudia Oliveira Carreira
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, SP, Brazil; Centre of Human and Natural Sciences, Federal University of ABC, Santo André, SP, Brazil
| | - Maria Angelica Miglino
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, SP, Brazil.
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Lin F, Li X, Sun S, Li Z, Lv C, Bai J, Song L, Han Y, Li B, Fu J, Shao Y. Mechanically enhanced biogenesis of gut spheroids with instability-driven morphomechanics. Nat Commun 2023; 14:6016. [PMID: 37758697 PMCID: PMC10533890 DOI: 10.1038/s41467-023-41760-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Region-specific gut spheroids are precursors for gastrointestinal and pulmonary organoids that hold great promise for fundamental studies and translations. However, efficient production of gut spheroids remains challenging due to a lack of control and mechanistic understanding of gut spheroid morphogenesis. Here, we report an efficient biomaterial system, termed micropatterned gut spheroid generator (μGSG), to generate gut spheroids from human pluripotent stem cells through mechanically enhanced tissue morphogenesis. We show that μGSG enhances the biogenesis of gut spheroids independent of micropattern shape and size; instead, mechanically enforced cell multilayering and crowding is demonstrated as a general, geometry-insensitive mechanism that is necessary and sufficient for promoting spheroid formation. Combining experimental findings and an active-phase-field morphomechanics theory, our study further reveals an instability-driven mechanism and a mechanosensitive phase diagram governing spheroid pearling and fission in μGSG. This work unveils mechanobiological paradigms based on tissue architecture and surface tension for controlling tissue morphogenesis and advancing organoid technology.
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Affiliation(s)
- Feng Lin
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Xia Li
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, China
| | - Shiyu Sun
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, China
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Zhongyi Li
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, China
| | - Chenglin Lv
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, China
| | - Jianbo Bai
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, China
| | - Lin Song
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Yizhao Han
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, China
| | - Bo Li
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, China.
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yue Shao
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, China.
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.
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Zwick RK, Kasparek P, Palikuqi B, Viragova S, Weichselbaum L, McGinnis CS, McKinley KL, Rathnayake A, Vaka D, Nguyen V, Trentesaux C, Reyes E, Gupta AR, Gartner ZJ, Locksley RM, Gardner JM, Itzkovitz S, Boffelli D, Klein OD. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558726. [PMID: 37790430 PMCID: PMC10542170 DOI: 10.1101/2023.09.20.558726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
A key aspect of nutrient absorption is the exquisite division of labor across the length of the small intestine, with individual classes of micronutrients taken up at different positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum, and ileum. By examining fine-scale longitudinal segmentation of the mouse and human small intestines, we identified transcriptional signatures and upstream regulatory factors that define five domains of nutrient absorption, distinct from the three traditional sections. Spatially restricted expression programs were most prominent in nutrient-absorbing enterocytes but initially arose in intestinal stem cells residing in three regional populations. While a core signature was maintained across mice and humans with different diets and environments, domain properties were influenced by dietary changes. We established the functions of Ppar-ẟ and Cdx1 in patterning lipid metabolism in distal domains and generated a predictive model of additional transcription factors that direct domain identity. Molecular domain identity can be detected with machine learning, representing the first systematic method to computationally identify specific intestinal regions in mice. These findings provide a foundational framework for the identity and control of longitudinal zonation of absorption along the proximal:distal small intestinal axis.
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Ma Z, Zhang X, Zhong W, Yi H, Chen X, Zhao Y, Ma Y, Song E, Xu T. Deciphering early human pancreas development at the single-cell level. Nat Commun 2023; 14:5354. [PMID: 37660175 PMCID: PMC10475098 DOI: 10.1038/s41467-023-40893-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 08/15/2023] [Indexed: 09/04/2023] Open
Abstract
Understanding pancreas development can provide clues for better treatments of pancreatic diseases. However, the molecular heterogeneity and developmental trajectory of the early human pancreas are poorly explored. Here, we performed large-scale single-cell RNA sequencing and single-cell assay for transposase accessible chromatin sequencing of human embryonic pancreas tissue obtained from first-trimester embryos. We unraveled the molecular heterogeneity, developmental trajectories and regulatory networks of the major cell types. The results reveal that dorsal pancreatic multipotent cells in humans exhibit different gene expression patterns than ventral multipotent cells. Pancreato-biliary progenitors that generate ventral multipotent cells in humans were identified. Notch and MAPK signals from mesenchymal cells regulate the differentiation of multipotent cells into trunk and duct cells. Notably, we identified endocrine progenitor subclusters with different differentiation potentials. Although the developmental trajectories are largely conserved between humans and mice, some distinct gene expression patterns have also been identified. Overall, we provide a comprehensive landscape of early human pancreas development to understand its lineage transitions and molecular complexity.
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Affiliation(s)
- Zhuo Ma
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570102, China
| | - Wen Zhong
- Science for Life Laboratory, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, 581 83, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Hongyan Yi
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570102, China
| | - Xiaowei Chen
- Center for High Throughput Sequencing, Core Facility for Protein Research, Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yinsuo Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanlin Ma
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Key Laboratory of Reproductive Health Diseases Research and Translation (Hainan Medical University), Ministry of Education, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 570102, China.
| | - Eli Song
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Tao Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Guangzhou Laboratory, Guangzhou, 510005, China.
- Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, China.
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China.
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35
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Montero E, Isenberg JS. The TSP1-CD47-SIRPα interactome: an immune triangle for the checkpoint era. Cancer Immunol Immunother 2023; 72:2879-2888. [PMID: 37217603 PMCID: PMC10412679 DOI: 10.1007/s00262-023-03465-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023]
Abstract
The use of treatments, such as programmed death protein 1 (PD1) or cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) antibodies, that loosen the natural checks upon immune cell activity to enhance cancer killing have shifted clinical practice and outcomes for the better. Accordingly, the number of antibodies and engineered proteins that interact with the ligand-receptor components of immune checkpoints continue to increase along with their use. It is tempting to view these molecular pathways simply from an immune inhibitory perspective. But this should be resisted. Checkpoint molecules can have other cardinal functions relevant to the development and use of blocking moieties. Cell receptor CD47 is an example of this. CD47 is found on the surface of all human cells. Within the checkpoint paradigm, non-immune cell CD47 signals through immune cell surface signal regulatory protein alpha (SIRPα) to limit the activity of the latter, the so-called trans signal. Even so, CD47 interacts with other cell surface and soluble molecules to regulate biogas and redox signaling, mitochondria and metabolism, self-renewal factors and multipotency, and blood flow. Further, the pedigree of checkpoint CD47 is more intricate than supposed. High-affinity interaction with soluble thrombospondin-1 (TSP1) and low-affinity interaction with same-cell SIRPα, the so-called cis signal, and non-SIRPα ectodomains on the cell membrane suggests that multiple immune checkpoints converge at and through CD47. Appreciation of this may provide latitude for pathway-specific targeting and intelligent therapeutic effect.
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Affiliation(s)
- Enrique Montero
- Department of Diabetes Immunology, City of Hope National Medical Center, 1500 Duarte Road, Duarte, CA, 91010, USA
- Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope National Medical Center, 1500 Duarte Road, Duarte, CA, 91010, USA
| | - Jeffrey S Isenberg
- Department of Diabetes Complications and Metabolism, City of Hope National Medical Center, 1500 Duarte Road, Duarte, CA, 91010, USA.
- Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope National Medical Center, 1500 Duarte Road, Duarte, CA, 91010, USA.
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36
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Tiwari SK, Rana TM. Generation of 3D lung organoids from human induced pluripotent stem cells for modeling of lung development and viral infection. Heliyon 2023; 9:e19601. [PMID: 37809493 PMCID: PMC10558843 DOI: 10.1016/j.heliyon.2023.e19601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/20/2023] [Accepted: 08/28/2023] [Indexed: 10/10/2023] Open
Abstract
The lack of physiologically relevant in vitro models has hampered progress in understanding human lung development and disease. Here, we describe a protocol in which human induced pluripotent stem cells (hiPSCs) undergo stepwise differentiation into definitive endoderm (>88% population) to three-dimensional (3D) lung organoids (LORGs), which contain both epithelial and mesenchymal cellular architecture and display proximal and distal airway patterning. These LORGs can maintained for more than 90 days by re-embedding in the Matrigel. We show the utility of LORGs for disease modeling and drug screening by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and treatment with antiviral drugs.
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Affiliation(s)
- Shashi Kant Tiwari
- Division of Genetics, Department of Pediatrics, Program in Immunology, Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA, 92093, USA
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37
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Reyes-Castro RA, Chen SY, Seemann J, Kundu ST, Gibbons DL, Arur S. Phosphorylated nuclear DICER1 promotes open chromatin state and lineage plasticity of AT2 tumor cells in lung adenocarcinomas. SCIENCE ADVANCES 2023; 9:eadf6210. [PMID: 37494452 PMCID: PMC10371025 DOI: 10.1126/sciadv.adf6210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
KRAS/ERK pathway phosphorylates DICER1, causing its nuclear translocation, and phosphomimetic Dicer1 contributes to tumorigenesis in mice. Mechanisms through which phospho-DICER1 regulates tumor progression remain undefined. While DICER1 canonically regulates microRNAs (miRNA) and epithelial-to-mesenchymal transition (EMT), we found that phosphorylated nuclear DICER1 (phospho-nuclear DICER1) promotes late-stage tumor progression in mice with oncogenic Kras, independent of miRNAs and EMT. Instead, we observe that the murine AT2 tumor cells exhibit altered chromatin compaction, and cells from disorganized advanced tumors, but not localized tumors, express gastric genes. Collectively, this results in subpopulations of tumor cells transitioning from a restricted alveolar to a broader endodermal lineage state. In human LUADs, we observed expression of phospho-nuclear DICER1 in advanced tumors together with the expression of gastric genes. We define a multimeric chromatin-DICER1 complex composed of the Mediator complex subunit 12, CBX1, MACROH2A.1, and transcriptional regulators supporting the model that phospho-nuclear DICER1 leads to lineage reprogramming of AT2 tumor cells to mediate lung cancer progression.
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Affiliation(s)
- Raisa A. Reyes-Castro
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- School of Medicine, University of Puerto Rico, San Juan, Puerto Rico
- Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center and UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Shin-Yu Chen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jacob Seemann
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samrat T. Kundu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Don L. Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Swathi Arur
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center and UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
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38
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Kolev HM, Kaestner KH. Mammalian Intestinal Development and Differentiation-The State of the Art. Cell Mol Gastroenterol Hepatol 2023; 16:809-821. [PMID: 37507088 PMCID: PMC10520362 DOI: 10.1016/j.jcmgh.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Abstract
The development of the mammalian intestine, from its earliest origins as a morphologically uniform sheet of endoderm cells during gastrulation into the complex organ system that is essential for the life of the organism, is a truly fascinating process. During midgestation development, reciprocal interactions between endoderm-derived epithelium and mesoderm-derived mesenchyme enable villification, or the conversion of a radially symmetric pseudostratified epithelium into the functional subdivision of crypts and villi. Once a mature crypt-villus axis is established, proliferation and differentiation of new epithelial cells continue throughout life. Spatially localized signals including the wingless and Int-1, fibroblast growth factor, and Hippo systems, among others, ensure that new cells are being born continuously in the crypt. As cells exit the crypt compartment, a gradient of bone morphogenetic protein signaling limits proliferation to allow for the specification of multiple mature cell types. The first major differentiation decision is dependent on Notch signaling, which specifies epithelial cells into absorptive and secretory lineages. The secretory lineage is subdivided further into Paneth, goblet, tuft, and enteroendocrine cells via a complex network of transcription factors. Although some of the signaling molecules are produced by epithelial cells, critical components are derived from specialized crypt-adjacent mesenchymal cells termed telocytes, which are marked by Forkhead box l1, GLI Family Zinc Finger 1, and platelet-derived growth factor receptor α. The crucial nature of these processes is evidenced by the multitude of intestinal disorders such as colorectal cancer, short-bowel syndrome, and inflammatory bowel disease, which all reflect perturbations of the development and/or differentiation of the intestine.
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Affiliation(s)
- Hannah M Kolev
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Klaus H Kaestner
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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Chen N, Shi L, Ge J, Jia R, Jiang J. Risk and prediction of multiple primary malignancies after early gastric cancer. Front Oncol 2023; 13:1205358. [PMID: 37560468 PMCID: PMC10409482 DOI: 10.3389/fonc.2023.1205358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Patients with early gastric cancer have increased risk of developing multiple primary malignancies (MPM) due to improved survival rates. The purpose of this study was to evaluate the clinicopathological features of MPM and to generate a useful tool for predicting the development of MPM after early gastric cancer. METHODS We selected 1025 early gastric cancer patients with complete medical records for a retrospective analysis. The Cox proportional risk regression model was used to analyze the independent risk factors for the development of MPM in early gastric cancer. RStudio software was used to compare the OS of early gastric cancer patients with and without MPM, and a nomogram was established to predict the probability of MPM 1-, 2-, 3-year after early gastric cancer. The predictive effectiveness of the nomogram was evaluated by the C-index and calibration curve. Decision curve analysis (DCA) measured the applicability of the nomogram to clinical practice. RESULTS Of the 1025 patients with early gastric cancer, 66 patients (6.4%) had 69 primary cancers other than early gastric cancer. They had a median follow-up of 41 months, and their cumulative incidence of MPM was 4.9%, 5.4% and 5.9% after 1-, 2-, and 3- year, respectively. Oesophageal cancer was the most frequently detected MPM, followed by lung and colorectal cancers. Male (p=0.038), age ≥65 years (p=0.003), smoking history (p=0.036), and lymph node metastasis (p=0.013) were independent risk factors for MPM in patients with early gastric cancer. Patients with early gastric cancer with MPM had a worse OS prognosis than patients with early gastric cancer without MPM (p<0.001). The internally validated nomogram predicted the probability of developing MPM after early gastric cancer (C index= 0.697). The calibration chart showed that the predicted probability of MPM in early gastric cancer was similar to the observed result, and the DCA showed strong clinical practicability. CONCLUSION After the diagnosis and treatment of early gastric cancer, we should be alert to the possibility of MPM and perform regular and careful monitoring.
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Affiliation(s)
| | | | | | | | - Junmei Jiang
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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40
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Frommelt J, Liu E, Bhaidani A, Hu B, Gao Y, Ye D, Lin F. Flat mount preparation for whole-mount fluorescent imaging of zebrafish embryos. Biol Open 2023; 12:bio060048. [PMID: 37746815 PMCID: PMC10373579 DOI: 10.1242/bio.060048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 09/26/2023] Open
Abstract
The zebrafish is a widely used model organism for biomedical research due to its ease of maintenance, external fertilization of embryos, rapid embryonic development, and availability of established genetic tools. One notable advantage of using zebrafish is the transparency of the embryos, which enables high-resolution imaging of specific cells, tissues, and structures through the use of transgenic and knock-in lines. However, as the embryo develops, multiple layers of tissue wrap around the lipid-enriched yolk, which can create a challenge to image tissues located deep within the embryo. While various methods are available, such as two-photon imaging, cryosectioning, vibratome sectioning, and micro-surgery, each of these has limitations. In this study, we present a novel deyolking method that allows for high-quality imaging of tissues that are obscured by other tissues and the yolk. Embryos are lightly fixed in 1% PFA to remove the yolk without damaging embryonic tissues and are then refixed in 4% PFA and mounted on custom-made bridged slides. This method offers a simple way to prepare imaging samples that can be subjected to further preparation, such as immunostaining. Furthermore, the bridged slides described in this study can be used for imaging tissue and organ preparations from various model organisms.
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Affiliation(s)
- Joseph Frommelt
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Emily Liu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Afraz Bhaidani
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Bo Hu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Yuanyuan Gao
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Ding Ye
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Fang Lin
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
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Diane A, Mohammed LI, Al-Siddiqi HH. Islets in the body are never flat: transitioning from two-dimensional (2D) monolayer culture to three-dimensional (3D) spheroid for better efficiency in the generation of functional hPSC-derived pancreatic β cells in vitro. Cell Commun Signal 2023; 21:151. [PMID: 37349801 PMCID: PMC10286450 DOI: 10.1186/s12964-023-01171-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/20/2023] [Indexed: 06/24/2023] Open
Abstract
Diabetes mellitus (DM), currently affecting more than 537 million people worldwide is a chronic disease characterized by impaired glucose metabolism resulting from a defect in insulin secretion, action, or both due to the loss or dysfunction of pancreatic β cells. Since cadaveric islet transplantation using Edmonton protocol has served as an effective intervention to restore normoglycaemia in T1D patients for months, stem cell-derived β cells have been explored for cell replacement therapy for diabetes. Thus, great effort has been concentrated by scientists on developing in vitro differentiation protocols to realize the therapeutic potential of hPSC-derived β cells. However, most of the 2D traditional monolayer culture could mainly generate insulin-producing β cells with immature phenotype. In the body, pancreatic islets are 3D cell arrangements with complex cell-cell and cell-ECM interactions. Therefore, it is important to consider the spatial organization of the cell in the culture environment. More recently, 3D cell culture platforms have emerged as powerful tools with huge translational potential, particularly for stem cell research. 3D protocols provide a better model to recapitulate not only the in vivo morphology, but also the cell connectivity, polarity, and gene expression mimicking more physiologically the in vivo cell niche. Therefore, the 3D culture constitutes a more relevant model that may help to fill the gap between in vitro and in vivo models. Interestingly, most of the 2D planar methodologies that successfully generated functional hPSC-derived β cells have switched to a 3D arrangement of cells from pancreatic progenitor stage either as suspension clusters or as aggregates, suggesting the effect of 3D on β cell functionality. In this review we highlight the role of dimensionality (2D vs 3D) on the differentiation efficiency for generation of hPSC-derived insulin-producing β cells in vitro. Consequently, how transitioning from 2D monolayer culture to 3D spheroid would provide a better model for an efficient generation of fully functional hPSC-derived β cells mimicking in vivo islet niche for diabetes therapy or drug screening. Video Abstract.
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Affiliation(s)
- Abdoulaye Diane
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.
| | - Layla Ibrahim Mohammed
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Heba H Al-Siddiqi
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
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42
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LaBelle J, Wyatt T, Woo S. Endodermal cells use contact inhibition of locomotion to achieve uniform cell dispersal during zebrafish gastrulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543209. [PMID: 37333383 PMCID: PMC10274714 DOI: 10.1101/2023.06.01.543209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The endoderm is one of the three primary germ layers that ultimately gives rise to the gastrointestinal and respiratory epithelia and other tissues. In zebrafish and other vertebrates, endodermal cells are initially highly migratory with only transient interactions among one other, but later converge together to form an epithelial sheet. Here, we show that during their early, migratory phase, endodermal cells actively avoid each other through contact inhibition of locomotion (CIL), a characteristic response consisting of 1) actin depolymerization and membrane retraction at the site of contact, 2) preferential actin polymerization along a cell-free edge, and 3) reorientation of migration away from the other cell. We found that this response is dependent on the Rho GTPase RhoA and EphA/ephrin-A signaling - expression of dominant-negative (DN) RhoA or treatment with the EphA inhibitor dasatinib resulted in behaviors consistent with loss of CIL, including increased contact duration times and decreased likelihood of migration reorientation after contact. Computational modeling predicted that CIL is required to achieve the efficient and uniform dispersal characteristic of endodermal cells. Consistent with our model, we found that loss of CIL via DN RhoA expression resulted in irregular clustering of cells within the endoderm. Together, our results suggest that endodermal cells use EphA2- and RhoA-dependent CIL as a cell dispersal and spacing mechanism, demonstrating how local interactions can give rise to tissue-scale patterns.
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Affiliation(s)
- Jesselynn LaBelle
- Quantiative and Systems Biology, University of California, Merced, CA USA
| | - Tom Wyatt
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS, Université de Paris, France
| | - Stephanie Woo
- Quantiative and Systems Biology, University of California, Merced, CA USA
- Department of Molecular Cell Biology, University of California, Merced, CA USA
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43
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Oikonomou P, Cirne HC, Nerurkar NL. A chemo-mechanical model of endoderm movements driving elongation of the amniote hindgut. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541363. [PMID: 37292966 PMCID: PMC10245718 DOI: 10.1101/2023.05.18.541363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
While mechanical and biochemical descriptions of development are each essential, integration of upstream morphogenic cues with downstream tissue mechanics remains understudied in many contexts during vertebrate morphogenesis. A posterior gradient of Fibroblast Growth Factor (FGF) ligands generates a contractile force gradient in the definitive endoderm, driving collective cell movements to form the hindgut. Here, we developed a two-dimensional chemo-mechanical model to investigate how mechanical properties of the endoderm and transport properties of FGF coordinately regulate this process. We began by formulating a 2-D reaction-diffusion-advection model that describes the formation of an FGF protein gradient due to posterior displacement of cells transcribing unstable Fgf8 mRNA during axis elongation, coupled with translation, diffusion, and degradation of FGF protein. This was used together with experimental measurements of FGF activity in the chick endoderm to inform a continuum model of definitive endoderm as an active viscous fluid that generates contractile stresses in proportion to FGF concentration. The model replicated key aspects of hindgut morphogenesis, confirms that heterogeneous - but isotropic - contraction is sufficient to generate large anisotropic cell movements, and provides new insight into how chemo-mechanical coupling across the mesoderm and endoderm coordinates hindgut elongation with outgrowth of the tailbud.
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Affiliation(s)
| | - Helena C. Cirne
- Department of Biomedical Engineering, Columbia University, New York NY 10027
| | - Nandan L. Nerurkar
- Department of Biomedical Engineering, Columbia University, New York NY 10027
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44
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Wang R, Kang N, Zhang W, Chen B, Xu S, Wu L. The developmental toxicity of PM2.5 on the early stages of fetal lung with human lung bud tip progenitor organoids. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 330:121764. [PMID: 37142209 DOI: 10.1016/j.envpol.2023.121764] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/15/2023] [Accepted: 05/02/2023] [Indexed: 05/06/2023]
Abstract
Exposure to air pollution has been proven to be associated with impaired fetal lung development. However, due to the lack of reliable human source models, it is still challenging to deeply understand the human fetal lung development under PM2.5 exposure. Here, we utilized human embryonic stem cell (hESC) line H9 to generate lung bud tip progenitor organoids (LPOs), a process that mimics early stages of fetal lung development including definitive endoderm (DE) formation, anterior foregut endoderm (AFE) differentiation and lung progenitor cell specification, to evaluate potential pulmonary developmental toxicity of PM2.5. We demonstrated that PM2.5 exposure the entire LPOs induction from hESCs significantly affected cellular proliferation of LPOs, and altered the expression of lung progenitor cell markers NKX2.1, SOX2 and SOX9, which are canonically defined subsequently proximal-distal airways specification. To explore the dynamic influences of PM2.5 exposure at different stages of LPOs specification, we also found that PM2.5 exposure significantly affected the expression of several transcriptional factors that are important for the differentiation of DE and AFE. Mechanistically, we suggested PM2.5-induced developmental toxicity to LPOs was partially linked with the Wnt/β-catenin signaling pathway. Therefore, our findings further emphasize the substantial health risks in the development of respiratory system associated with prenatal exposure to PM2.5.
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Affiliation(s)
- Run Wang
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Ningning Kang
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, PR China
| | - Wen Zhang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Biao Chen
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Shengmin Xu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China.
| | - Lijun Wu
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China; Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
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45
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Singh A, Poling HM, Chaturvedi P, Thorner K, Sundaram N, Kechele DO, Childs CJ, McCauley HA, Fisher GW, Brown NE, Spence JR, Wells JM, Helmrath MA. Transplanted human intestinal organoids: a resource for modeling human intestinal development. Development 2023; 150:dev201416. [PMID: 37070767 PMCID: PMC10259511 DOI: 10.1242/dev.201416] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/28/2023] [Indexed: 04/19/2023]
Abstract
The in vitro differentiation of pluripotent stem cells into human intestinal organoids (HIOs) has served as a powerful means for creating complex three-dimensional intestinal structures. Owing to their diverse cell populations, transplantation into an animal host is supported with this system and allows the temporal formation of fully laminated structures, including crypt-villus architecture and smooth muscle layers that resemble native human intestine. Although the endpoint of HIO engraftment has been well described, here we aim to elucidate the developmental stages of HIO engraftment and establish whether it parallels fetal human intestinal development. We analyzed a time course of transplanted HIOs histologically at 2, 4, 6 and 8 weeks post-transplantation, and demonstrated that HIO maturation closely resembles key stages of fetal human intestinal development. We also utilized single-nuclear RNA sequencing to determine and track the emergence of distinct cell populations over time, and validated our transcriptomic data through in situ protein expression. These observations suggest that transplanted HIOs do indeed recapitulate early intestinal development, solidifying their value as a human intestinal model system.
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Affiliation(s)
- Akaljot Singh
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Holly M. Poling
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Praneet Chaturvedi
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Konrad Thorner
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Nambirajan Sundaram
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Daniel O. Kechele
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Charlie J. Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Heather A. McCauley
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Garrett W. Fisher
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Nicole E. Brown
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - James M. Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael A. Helmrath
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Center for Stem Cell and Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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Teague S, Primavera G, Chen B, Freeburne E, Khan H, Jo K, Johnson C, Heemskerk I. The time integral of BMP signaling determines fate in a stem cell model for early human development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536068. [PMID: 37090515 PMCID: PMC10120633 DOI: 10.1101/2023.04.10.536068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
How paracrine signals are interpreted to yield multiple cell fate decisions in a dynamic context during human development in vivo and in vitro remains poorly understood. Here we report an automated tracking method to follow signaling histories linked to cell fate in large numbers of human pluripotent stem cells (hPSCs). Using an unbiased statistical approach, we discovered that measured BMP signaling history correlates strongly with fate in individual cells. We found that BMP response in hPSCs varies more strongly in the duration of signaling than the level. However, we discovered that both the level and duration of signaling activity control cell fate choices only by changing the time integral of signaling and that duration and level are therefore interchangeable in this context. In a stem cell model for patterning of the human embryo, we showed that signaling histories predict the fate pattern and that the integral model correctly predicts changes in cell fate domains when signaling is perturbed. Using an RNA-seq screen we then found that mechanistically, BMP signaling is integrated by SOX2.
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Affiliation(s)
- Seth Teague
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Gillian Primavera
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Bohan Chen
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Emily Freeburne
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Hina Khan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kyoung Jo
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Craig Johnson
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Idse Heemskerk
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
- Center for Cell Plasticity and Organ Design, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Physics, University of Michigan, Ann Arbor, Michigan
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Tatum R, Wong D, Martins PN, Tchantchaleishvili V. Current status and future directions in the development and optimization of thoracic and abdominal artificial organs. Artif Organs 2023; 47:451-458. [PMID: 36421073 DOI: 10.1111/aor.14458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/18/2022] [Accepted: 11/06/2022] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Artificial organs are engineered devices with the capacity to be implanted or integrated into a living body to replace a failing organ, or to duplicate or augment one or multiple functions of the diseased organ. AREAS COVERED We evaluate the present landscape and future possibilities of artificial organ engineering by exploring the spectrum of four distinguishable device features: mobility, compatibility, functionality, and material composition. These mechanical and functional differences provide the framework through which we examine the current status and future possibilities of the abdominal and thoracic artificial organs. EXPERT OPINION Transforming the artificial organs landscape in ways that expand the scope of existing device capabilities and improve the clinical utility of artificial organs will require making improvements upon existing technologies and multidisciplinary cooperation to create and discover new capacities.
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Affiliation(s)
- Robert Tatum
- Division of Cardiac Surgery, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Daniella Wong
- Division of Cardiac Surgery, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Paulo N Martins
- Division of Cardiac Surgery, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Vakhtang Tchantchaleishvili
- Division of Cardiac Surgery, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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48
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Zhang M, Liu J, Mao A, Ning G, Cao Y, Zhang W, Wang Q. Tmem88 confines ectodermal Wnt2bb signaling in pharyngeal arch artery progenitors for balancing cell cycle progression and cell fate decision. NATURE CARDIOVASCULAR RESEARCH 2023; 2:234-250. [PMID: 39195996 DOI: 10.1038/s44161-023-00215-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 01/06/2023] [Indexed: 08/29/2024]
Abstract
Pharyngeal arch artery (PAA) progenitors undergo proliferative expansion and angioblast differentiation to build vessels connecting the heart with the dorsal aortae. However, it remains unclear whether and how these two processes are orchestrated. Here we demonstrate that Tmem88 is required to fine-tune PAA progenitor proliferation and differentiation. Loss of zebrafish tmem88a/b leads to an excessive expansion and a failure of differentiation of PAA progenitors. Moreover, tmem88a/b deficiency enhances cyclin D1 expression in PAA progenitors via aberrant Wnt signal activation. Mechanistically, cyclin D1-CDK4/6 promotes progenitor proliferation through accelerating the G1/S transition while suppressing angioblast differentiation by phosphorylating Nkx2.5/Smad3. Ectodermal Wnt2bb signaling is confined by Tmem88 in PAA progenitors to ensure a balance between proliferation and differentiation. Therefore, the proliferation and angioblast differentiation of PAA progenitors manifest an inverse relationship and are delicately regulated by cell cycle machinery downstream of the Tmem88-Wnt pathway.
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Affiliation(s)
- Mingming Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jie Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Aihua Mao
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guozhu Ning
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yu Cao
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wenqing Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Qiang Wang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China.
- Department of Hematology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China.
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49
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Nakajima H, Ishikawa H, Yamamoto T, Chiba A, Fukui H, Sako K, Fukumoto M, Mattonet K, Kwon HB, Hui SP, Dobreva GD, Kikuchi K, Helker CSM, Stainier DYR, Mochizuki N. Endoderm-derived islet1-expressing cells differentiate into endothelial cells to function as the vascular HSPC niche in zebrafish. Dev Cell 2023; 58:224-238.e7. [PMID: 36693371 DOI: 10.1016/j.devcel.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 10/26/2022] [Accepted: 12/29/2022] [Indexed: 01/25/2023]
Abstract
Endothelial cells (ECs) line blood vessels and serve as a niche for hematopoietic stem and progenitor cells (HSPCs). Recent data point to tissue-specific EC specialization as well as heterogeneity; however, it remains unclear how ECs acquire these properties. Here, by combining live-imaging-based lineage-tracing and single-cell transcriptomics in zebrafish embryos, we identify an unexpected origin for part of the vascular HSPC niche. We find that islet1 (isl1)-expressing cells are the progenitors of the venous ECs that constitute the majority of the HSPC niche. These isl1-expressing cells surprisingly originate from the endoderm and differentiate into ECs in a process dependent on Bmp-Smad signaling and subsequently requiring npas4l (cloche) function. Single-cell RNA sequencing analyses show that isl1-derived ECs express a set of genes that reflect their distinct origin. This study demonstrates that endothelial specialization in the HSPC niche is determined at least in part by the origin of the ECs.
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Affiliation(s)
- Hiroyuki Nakajima
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan.
| | - Hiroyuki Ishikawa
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; AMED-CREST, AMED, Tokyo 100-0004, Japan; Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Ayano Chiba
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Hajime Fukui
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Keisuke Sako
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Moe Fukumoto
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Kenny Mattonet
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Hyouk-Bum Kwon
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Subhra P Hui
- S. N. Pradhan Centre for Neurosciences, University of Calcutta, Kolkata 700019, India
| | - Gergana D Dobreva
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Kazu Kikuchi
- Department of Cardiac Regeneration Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Christian S M Helker
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany; Philipps-University Marburg, Faculty of Biology, Cell Signaling and Dynamics, Marburg 35043, Germany
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany.
| | - Naoki Mochizuki
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan.
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50
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Du X, Dong Y, Li W, Chen Y. hPSC-derived lung organoids: Potential opportunities and challenges. Heliyon 2023; 9:e13498. [PMID: 36814627 PMCID: PMC9939602 DOI: 10.1016/j.heliyon.2023.e13498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Three-dimensional hPSC-derived lung organoids resemble the fetal lung stage, making them an excellent model for studying human lung development. However, current hPSC-derived lung organoids remain incomplete as they lack native lung components such as vasculature, neurons and immune cells. This highlights the need to generate more complex hPSC-derived lung organoids that can faithfully mimic native human lungs for studying human lung development, regeneration, disease modeling and drug screen. In this review, we will discuss the current studies related to the generation of hPSC-derived lung organoids, highlighting how hPSC-derived lung organoids can contribute to the understanding of human lung development. We further focus on potential approaches to generate more complex hPSC-derived lung organoids containing native cellular components. Finally, we discuss the present limitations and potential applications of hPSC-derived lung organoids in the future.
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Affiliation(s)
- Xiaoli Du
- Department of Hematology, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Yongpin Dong
- Department of Emergency and Critical Care, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Wenfang Li
- Department of Emergency and Critical Care, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China,Corresponding author.
| | - Yong Chen
- Central Laboratory, Guizhou Provincial People's Hospital, Guiyang 550002, China,Corresponding author.
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