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Yang W, Li Z, Li Y, He W, Yan J. Transforming Albumin into a Trojan Horse of Immunotherapy-Resistant Colorectal Cancer with a High Microsatellite Instability. ACS NANO 2024. [PMID: 38990329 DOI: 10.1021/acsnano.4c05893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
The therapeutic response of microsatellite instability-high (MSI-H) colorectal cancer (CRC) to immune checkpoint inhibitors (ICI) is indeed surprising; however, the emergence of acquired resistance poses an even greater threat to the survival of these patients. Herein, bioinformatics analysis of MSI-H CRC samples revealed that Wnt signaling pathway represents a promising target for acquired immune reactivation, while subsequent analysis and biochemical testing substantiated the inclination of Wnt-hyperactive CRC cells to engage in macropinocytosis with human serum albumin (HSA). These findings have inspired us to develop an engineered HSA that not only possesses the ability to specifically target cancer cells but also effectively suppresses the Wnt/β-catenin cascade within these malignant cells. In pursuit of this objective, a comprehensive screening of reported Wnt small-molecule inhibitors was conducted to evaluate their affinity with HSA, and it was discovered that Carnosic acid (CA) exhibited the highest affinity while simultaneously revealing multiple binding sites. Further investigation revealed that CA HSA the capability to engineer HSA into spherical and size-tunable nanostructures known as eHSA (Engineering HSA particle), which demonstrated optimized macropinocytosis-dependent cellular internalization. As anticipated, eHSA effectively suppressed the Wnt signaling pathway and reactivated the acquired immune response in vivo. Furthermore, eHSA successfully restored sensitivity to Anti-PD1's anticancer effects in both subcutaneous and orthotopic mouse homograft models of MSI-H CRC, as well as a humanized hu-PBMC patient-derived orthotopic xenograft (PDOX) mouse model of MSI-H CRC, all while maintaining a favorable safety profile. The collective implementation of this clinically viable immune reactivation strategy not only enables the delivery of Wnt inhibitors for CRC therapy, but also serves as an exemplary demonstration of precision-medicine-guided nanopharmaceutical development that effectively harnesses specific cellular indications in pathological states.
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Affiliation(s)
- Wenguang Yang
- Department of Medical Oncology and Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR. China
| | - Zhanfeng Li
- Department of Medical Oncology and Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR. China
| | - Yong Li
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, PR. China
| | - Wangxiao He
- Department of Medical Oncology and Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR. China
| | - Jin Yan
- Department of Medical Oncology and Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR. China
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, PR. China
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
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2
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Xiao QX, Geng MJ, Sun YF, Pi Y, Xiong LL. Stem Cell Therapy in Neonatal Hypoxic-Ischemic Encephalopathy and Cerebral Palsy: a Bibliometric Analysis and New Strategy. Mol Neurobiol 2024; 61:4538-4564. [PMID: 38102517 DOI: 10.1007/s12035-023-03848-0] [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: 08/07/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
The aim of this study was to identify related scientific outputs and emerging topics of stem cells in neonatal hypoxic-ischemic encephalopathy (NHIE) and cerebral palsy (CP) through bibliometrics and literature review. All relevant publications on stem cell therapy for NHIE and CP were screened from websites and analyzed research trends. VOSviewer and CiteSpace were applied to visualize and quantitatively analyze the published literature to provide objective presentation and prediction. In addition, the clinical trials, published articles, and projects of the National Natural Science Foundation of China associated with stem cell therapy for NHIE and CP were summarized. A total of 294 publications were associated with stem cell therapy for NHIE and CP. Most publications and citations came from the USA and China. Monash University and University Medical Center Utrecht produced the most publications. Pediatric research published the most studies on stem cell therapy for NHIE and CP. Heijnen C and Kavelaars A published the most articles. Cluster analyses show that current research trend is more inclined toward the repair mechanism and clinical translation of stem cell therapy for NHIE and CP. By summarizing various studies of stem cells in NHIE and CP, it is indicated that this research direction is a hot topic at present. Furthermore, organoid transplantation, as an emerging and new therapeutic approach, brings new hope for the treatment of NHIE and CP. This study comprehensively summarized and analyzed the research trend of global stem cell therapy for NHIE and CP. It has shown a marked increase in stem cell therapy for NHIE and CP research. In the future, more efforts will be made on exploring stem cell or organoid therapy for NHIE and CP and more valuable related mechanisms of action to achieve clinical translation as soon as possible.
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Affiliation(s)
- Qiu-Xia Xiao
- Department of Anesthesiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Min-Jian Geng
- Department of Anesthesiology, Nanchong Central Hospital, Nanchong, 637000, Sichuan, China
| | - Yi-Fei Sun
- Institute of Neurological Disease, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yu Pi
- Department of Anesthesiology, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Liu-Lin Xiong
- Department of Anesthesiology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China.
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3
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Şişli HB, Şenkal Turhan S, Bulut Okumuş E, Böke ÖB, Erdoğmuş Ö, Kül B, Sümer E, Doğan A. Azoxymethane-induced carcinogenesis-like model of mouse intestine and mouse embryonic stem cell-derived intestinal organoids. Mol Biol Rep 2024; 51:704. [PMID: 38824233 DOI: 10.1007/s11033-024-09660-w] [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: 03/15/2024] [Accepted: 05/21/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Tumor modeling using organoids holds potential in studies of cancer development, enlightening both the intracellular and extracellular molecular mechanisms behind different cancer types, biobanking, and drug screening. Intestinal organoids can be generated in vitro using a unique type of adult stem cells which are found at the base of crypts and are characterized by their high Lgr5 expression levels. METHODS AND RESULTS In this study, we successfully established intestinal cancer organoid models by using both the BALB/c derived and mouse embryonic stem cells (mESCs)-derived intestinal organoids. In both cases, carcinogenesis-like model was developed by using azoxymethane (AOM) treatment. Carcinogenesis-like model was verified by H&E staining, immunostaining, relative mRNA expression analysis, and LC/MS analysis. The morphologic analysis demonstrated that the number of generated organoids, the number of crypts, and the intensity of the organoids were significantly augmented in AOM-treated intestinal organoids compared to non-AOM-treated ones. Relative mRNA expression data revealed that there was a significant increase in both Wnt signaling pathway-related genes and pluripotency transcription factors in the AOM-induced intestinal organoids. CONCLUSION We successfully developed simple carcinogenesis-like models using mESC-based and Lgr5 + stem cell-based intestinal organoids. Intestinal organoid based carcinogenesi models might be used for personalized cancer therapy in the future.
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Affiliation(s)
- Hatice Burcu Şişli
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - Selinay Şenkal Turhan
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - Ezgi Bulut Okumuş
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - Özüm Begüm Böke
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - Özüm Erdoğmuş
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - Berke Kül
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - Engin Sümer
- Faculty of Medicine, Experimental Research Center, Yeditepe University, Istanbul, Turkey
| | - Ayşegül Doğan
- Faculty of Engineering, Genetics and Bioengineering Department, Yeditepe University, Istanbul, Turkey.
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4
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Pothuraju R, Khan I, Jain M, Bouvet M, Malafa M, Roy HK, Kumar S, Batra SK. Colorectal cancer murine models: Initiation to metastasis. Cancer Lett 2024; 587:216704. [PMID: 38360138 DOI: 10.1016/j.canlet.2024.216704] [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: 10/23/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
Despite significant advancements in prevention and treatment, colorectal cancer (CRC) remains the third leading cause of cancer-related deaths. Animal models, including xenografts, syngeneic, and genetically engineered, have emerged as indispensable tools in cancer research. These models offer a valuable platform to address critical questions regarding molecular pathogenesis and test therapeutic interventions before moving on to clinical trials. Advancements in CRC animal models have also facilitated the advent of personalized and precision medicine. Patient-derived xenografts and genetically engineered mice that mirror features of human tumors allow for tailoring treatments to specific CRC subtypes, improving treatment outcomes and quality of life. To overcome the limitations of individual model systems, recent studies have employed a multi-modal approach, combining different animal models, 3D organoids, and in vitro studies. This integrative approach provides a comprehensive understanding of CRC biology, including the tumor microenvironment and therapeutic responses, driving the development of more effective and personalized therapeutic interventions. This review discusses the animal models used for CRC research, including recent advancements and limitations of these animal models.
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Affiliation(s)
- Ramesh Pothuraju
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, Kerala, India
| | - Imran Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Michael Bouvet
- Department of Surgery, University of California San Diego, California, USA
| | - Mokenge Malafa
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Hemant K Roy
- Department of Medicine, Baylor College of Medicine, Houston, TX-77030, USA
| | - Sushil Kumar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA.
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE-68198, USA.
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5
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Guo L, Li C, Gong W. Toward reproducible tumor organoid culture: focusing on primary liver cancer. Front Immunol 2024; 15:1290504. [PMID: 38571961 PMCID: PMC10987700 DOI: 10.3389/fimmu.2024.1290504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024] Open
Abstract
Organoids present substantial potential for pushing forward preclinical research and personalized medicine by accurately recapitulating tissue and tumor heterogeneity in vitro. However, the lack of standardized protocols for cancer organoid culture has hindered reproducibility. This paper comprehensively reviews the current challenges associated with cancer organoid culture and highlights recent multidisciplinary advancements in the field with a specific focus on standardizing liver cancer organoid culture. We discuss the non-standardized aspects, including tissue sources, processing techniques, medium formulations, and matrix materials, that contribute to technical variability. Furthermore, we emphasize the need to establish reproducible platforms that accurately preserve the genetic, proteomic, morphological, and pharmacotypic features of the parent tumor. At the end of each section, our focus shifts to organoid culture standardization in primary liver cancer. By addressing these challenges, we can enhance the reproducibility and clinical translation of cancer organoid systems, enabling their potential applications in precision medicine, drug screening, and preclinical research.
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Affiliation(s)
| | | | - Weiqiang Gong
- Department of Hepatobiliary and Pancreatic Surgery, Weifang People’s Hospital, Weifang, Shandong, China
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6
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Lee J, Heo SC, Kim Y. Combination of oxaliplatin and β-carotene suppresses colorectal cancer by regulating cell cycle, apoptosis, and cancer stemness in vitro. Nutr Res Pract 2024; 18:62-77. [PMID: 38352212 PMCID: PMC10861335 DOI: 10.4162/nrp.2024.18.1.62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/12/2023] [Accepted: 12/06/2023] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND/OBJECTIVES Colorectal cancer (CRC) is the third most common cancer worldwide with a high recurrence rate. Oxaliplatin (OXA) resistance is one of the major reasons hindering CRC therapy. β-Carotene (BC) is a provitamin A and is known to have antioxidant and anticancer effects. However, the combined effect of OXA and BC has not been investigated. Therefore, this study investigated the anticancer effects and mechanism of the combination of OXA and BC on CRC. MATERIALS/METHODS In the present study, the effects of the combination of OXA and BC on cell viability, cell cycle arrest, and cancer stemness were investigated using HCT116, HT29, OXA-resistant cells, and human CRC organoids. RESULTS The combination of OXA and BC enhanced apoptosis, G2/M phase cell cycle arrest, and inhibited cancer cell survival in human CRC resistant cells and CRC organoids without toxicity in normal organoids. Cancer stem cell marker expression and self-replicating capacity were suppressed by combined treatment with OXA and BC. Moreover, this combined treatment upregulated apoptosis and the stem cell-related JAK/STAT signaling pathway. CONCLUSIONS Our results suggest a novel potential role of BC in reducing resistance to OXA, thereby enhances the anticancer effects of OXA. This enhancement is achieved through the regulation of cell cycle, apoptosis, and stemness in CRC.
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Affiliation(s)
- Junghyeun Lee
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Korea
| | - Seung Chul Heo
- Department of Surgery, Seoul National University-Seoul Metropolitan Government (SNU-SMG) Boramae Medical Center, Seoul 07061, Korea
| | - Yuri Kim
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Korea
- Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Korea
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7
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Majumder J, Torr EE, Aisenbrey EA, Lebakken CS, Favreau PF, Richards WD, Yin Y, Chang Q, Murphy WL. Human induced pluripotent stem cell-derived planar neural organoids assembled on synthetic hydrogels. J Tissue Eng 2024; 15:20417314241230633. [PMID: 38361535 PMCID: PMC10868488 DOI: 10.1177/20417314241230633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/20/2024] [Indexed: 02/17/2024] Open
Abstract
The tailorable properties of synthetic polyethylene glycol (PEG) hydrogels make them an attractive substrate for human organoid assembly. Here, we formed human neural organoids from iPSC-derived progenitor cells in two distinct formats: (i) cells seeded on a Matrigel surface; and (ii) cells seeded on a synthetic PEG hydrogel surface. Tissue assembly on synthetic PEG hydrogels resulted in three dimensional (3D) planar neural organoids with greater neuronal diversity, greater expression of neurovascular and neuroinflammatory genes, and reduced variability when compared with tissues assembled upon Matrigel. Further, our 3D human tissue assembly approach occurred in an open cell culture format and created a tissue that was sufficiently translucent to allow for continuous imaging. Planar neural organoids formed on PEG hydrogels also showed higher expression of neural, vascular, and neuroinflammatory genes when compared to traditional brain organoids grown in Matrigel suspensions. Further, planar neural organoids contained functional microglia that responded to pro-inflammatory stimuli, and were responsive to anti-inflammatory drugs. These results demonstrate that the PEG hydrogel neural organoids can be used as a physiologically relevant in vitro model of neuro-inflammation.
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Affiliation(s)
- Joydeb Majumder
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth E Torr
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth A Aisenbrey
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | - Yanhong Yin
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Qiang Chang
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
- Departments of Medical Genetics and Neurology, University of Wisconsin-Madison, Madison, WI, USA
| | - William L Murphy
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
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8
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Zhang W, Jin H, Lou S, Yang H, Dai X, Ma S. Microfluidic droplet encapsulation-guided organoid growth promotes parental tumor phenotype recapitulation. Int J Cancer 2024; 154:145-154. [PMID: 37622267 DOI: 10.1002/ijc.34706] [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: 05/30/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023]
Abstract
Patient-derived organoids are gaining incremental popularity in both basic sciences and translational applications toward precision medicine and revolutionized drug discovery. However, for tumor organoids, challenges remain in low rates of organoid growth and tumor cell purity, that is, recapitulation of tumor phenotypes in constructed organoids. Here, we report a method of microfluidic droplet encapsulation that provides structural guidance for tumor cell growth and organization, where they develop into tumor organoids with high purity and high rates of modeling success, as compared to the classical organoid modeling method, that is, non-engineered organoids. The modeling efficacy and organoid quality are examined in patient-derived samples, covering esophagus, lung and colorectal cancer tissues, all proving significance in droplet-engineered organoids, as demonstrated by histological examinations.
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Affiliation(s)
- Weijie Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - He Jin
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen, China
| | - Shitong Lou
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haowei Yang
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen, China
| | - Xiaoyong Dai
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen, China
| | - Shaohua Ma
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen, China
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9
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Hu Y, Liu L, Jiang Q, Fang W, Chen Y, Hong Y, Zhai X. CRISPR/Cas9: a powerful tool in colorectal cancer research. J Exp Clin Cancer Res 2023; 42:308. [PMID: 37993945 PMCID: PMC10664500 DOI: 10.1186/s13046-023-02901-z] [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: 09/14/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant cancers worldwide and seriously threatens human health. The clustered regulatory interspaced short palindromic repeat/CRISPR-associate nuclease 9 (CRISPR/Cas9) system is an adaptive immune system of bacteria or archaea. Since its introduction, research into various aspects of treatment approaches for CRC has been accelerated, including investigation of the oncogenes, tumor suppressor genes (TSGs), drug resistance genes, target genes, mouse model construction, and especially in genome-wide library screening. Furthermore, the CRISPR/Cas9 system can be utilized for gene therapy for CRC, specifically involving in the molecular targeted drug delivery or targeted knockout in vivo. In this review, we elucidate the mechanism of the CRISPR/Cas9 system and its comprehensive applications in CRC. Additionally, we discussed the issue of off-target effects associated with CRISPR/Cas9, which serves to restrict its practical application. Future research on CRC should in-depth and systematically utilize the CRISPR/Cas9 system thereby achieving clinical practice.
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Affiliation(s)
- Yang Hu
- Department of Gastroenterology, The First People's Hospital of Jiande, Hangzhou, 311600, China
| | - Liang Liu
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Qi Jiang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Weiping Fang
- Department of Gastroenterology, The First People's Hospital of Jiande, Hangzhou, 311600, China
| | - Yazhu Chen
- West China Hospital of Sichuan University, Chengdu, 610044, China.
| | - Yuntian Hong
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Xiang Zhai
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
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10
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Farin HF, Mosa MH, Ndreshkjana B, Grebbin BM, Ritter B, Menche C, Kennel KB, Ziegler PK, Szabó L, Bollrath J, Rieder D, Michels BE, Kress A, Bozlar M, Darvishi T, Stier S, Kur IM, Bankov K, Kesselring R, Fichtner-Feigl S, Brüne B, Goetze TO, Al-Batran SE, Brandts CH, Bechstein WO, Wild PJ, Weigert A, Müller S, Knapp S, Trajanoski Z, Greten FR. Colorectal Cancer Organoid-Stroma Biobank Allows Subtype-Specific Assessment of Individualized Therapy Responses. Cancer Discov 2023; 13:2192-2211. [PMID: 37489084 PMCID: PMC10551667 DOI: 10.1158/2159-8290.cd-23-0050] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/05/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
In colorectal cancers, the tumor microenvironment plays a key role in prognosis and therapy efficacy. Patient-derived tumor organoids (PDTO) show enormous potential for preclinical testing; however, cultured tumor cells lose important characteristics, including the consensus molecular subtypes (CMS). To better reflect the cellular heterogeneity, we established the colorectal cancer organoid-stroma biobank of matched PDTOs and cancer-associated fibroblasts (CAF) from 30 patients. Context-specific phenotyping showed that xenotransplantation or coculture with CAFs improves the transcriptomic fidelity and instructs subtype-specific stromal gene expression. Furthermore, functional profiling in coculture exposed CMS4-specific therapeutic resistance to gefitinib and SN-38 and prognostic expression signatures. Chemogenomic library screening identified patient- and therapy-dependent mechanisms of stromal resistance including MET as a common target. Our results demonstrate that colorectal cancer phenotypes are encrypted in the cancer epithelium in a plastic fashion that strongly depends on the context. Consequently, CAFs are essential for a faithful representation of molecular subtypes and therapy responses ex vivo. SIGNIFICANCE Systematic characterization of the organoid-stroma biobank provides a resource for context dependency in colorectal cancer. We demonstrate a colorectal cancer subtype memory of PDTOs that is independent of specific driver mutations. Our data underscore the importance of functional profiling in cocultures for improved preclinical testing and identification of stromal resistance mechanisms. This article is featured in Selected Articles from This Issue, p. 2109.
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Affiliation(s)
- Henner F. Farin
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mohammed H. Mosa
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Benardina Ndreshkjana
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Britta M. Grebbin
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Birgit Ritter
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Constantin Menche
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Kilian B. Kennel
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Paul K. Ziegler
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Lili Szabó
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Julia Bollrath
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Dietmar Rieder
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Birgitta E. Michels
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Alena Kress
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Müge Bozlar
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Tahmineh Darvishi
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Sara Stier
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Ivan-Maximilano Kur
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- Institute of Biochemistry I, Goethe University, Frankfurt am Main, Germany
| | - Katrin Bankov
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Rebecca Kesselring
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of General and Visceral Surgery, University of Freiburg, Freiburg, Germany
| | - Stefan Fichtner-Feigl
- Department of General and Visceral Surgery, University of Freiburg, Freiburg, Germany
| | - Bernhard Brüne
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Biochemistry I, Goethe University, Frankfurt am Main, Germany
| | | | | | - Christian H. Brandts
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Wolf O. Bechstein
- Department of General and Visceral Surgery, Goethe University, Frankfurt am Main, Germany
| | - Peter J. Wild
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies (FIAS), Frankfurt am Main, Germany
| | - Andreas Weigert
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Biochemistry I, Goethe University, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe University, Frankfurt am Main, Germany
| | - Stefan Knapp
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe University, Frankfurt am Main, Germany
| | - Zlatko Trajanoski
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian R. Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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11
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Kishore C, Zi X. Wnt Signaling and Therapeutic Resistance in Castration-Resistant Prostate Cancer. CURRENT PHARMACOLOGY REPORTS 2023; 9:261-274. [PMID: 37994344 PMCID: PMC10664806 DOI: 10.1007/s40495-023-00333-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 11/24/2023]
Abstract
Purpose of Review Castration-resistant prostate cancer (CRPC) is a lethal form of prostate cancer (PCa) due to the development of resistance to androgen deprivation therapy and anti-androgens. Here, we review the emerging role of Wnt signaling in therapeutic resistance of CRPC. Recent Findings Convincing evidence have accumulated that Wnt signaling is aberrantly activated through genomic alterations and autocrine and paracrine augmentations. Wnt signaling plays a critical role in a subset of CRPC and in resistance to anti-androgen therapies. Wnt signaling navigates CRPC through PCa heterogeneity, neuroendocrine differentiation, DNA repair, PCa stem cell maintenance, epithelial-mesenchymal-transition and metastasis, and immune evasion. Summary Components of Wnt signaling can be harnessed for inhibiting PCa growth and metastasis and for developing novel therapeutic strategies to manage metastatic CRPC. There are many Wnt pathway-based potential drugs in different stages of pre-clinical development and clinical trials but so far, no Wnt signaling-specific drug has been approved by FDA for clinical use in CRPC.
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Affiliation(s)
- Chandra Kishore
- Department of Urology, University of California, Irvine, 101 The City Drive South, Rt.81 Bldg.55 Rm.204, Orange, CA 92868, USA
| | - Xiaolin Zi
- Department of Urology, University of California, Irvine, 101 The City Drive South, Rt.81 Bldg.55 Rm.204, Orange, CA 92868, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92868, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92617, USA
- Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA
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12
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Liu Y, Gao Q, Feng X, Chen G, Jiang X, Chen D, Yang Z. Aquaporin 9 is involved in CRC metastasis through DVL2-dependent Wnt/β-catenin signaling activation. Gastroenterol Rep (Oxf) 2023; 11:goad033. [PMID: 37360194 PMCID: PMC10287913 DOI: 10.1093/gastro/goad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/11/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Background Aquaporin 9 (AQP9) is permeable to water or other small molecules, and plays an important role in various cancers. We previously found that AQP9 was related to the efficacy of chemotherapy in patients with colorectal cancer (CRC). This study aimed to identify the role and regulatory mechanism of AQP9 in CRC metastasis. Methods The clinical significance of AQP9 was analysed by using bioinformatics and tissue microarray. Transcriptome sequencing, Dual-Luciferase Reporter Assay, Biacore, and co-immunoprecipitation were employed to demonstrate the regulatory mechanism of AQP9 in CRC. The relationship between AQP9 and CRC metastasis was verified in vitro and in vivo by using real-time cell analysis assay, high content screening, and liver metastasis models of nude mice. Results We found that AQP9 was highly expressed in metastatic CRC. AQP9 overexpression reduced cell roundness and enhanced cell motility in CRC. We further showed that AQP9 interacted with Dishevelled 2 (DVL2) via the C-terminal SVIM motif, resulting in DVL2 stabilization and the Wnt/β-catenin pathway activation. Additionally, we identified the E3 ligase neural precursor cell expressed developmentally downregulated 4-like (NEDD4L) as a modulator regulating the ubiquitination and degradation of AQP9. Conclusions Collectively, our study revealed the important role of AQP9 in regulating DVL2 stabilization and Wnt/β-catenin signaling to promote CRC metastasis. Targeting the NEDD4L-AQP9-DVL2 axis might have therapeutic usefulness in metastatic CRC treatment.
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Affiliation(s)
| | | | | | - Guanxing Chen
- Artificial Intelligence Medical Research Center, School of Intelligent Systems Engineering, Sun Yat-sen University, Shenzhen, Guangdong, P. R. China
| | - Xuefei Jiang
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, Guangdong, P. R. China
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Daici Chen
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangzhou, Guangdong, P. R. China
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Zihuan Yang
- Corresponding author. Department of Clinical Laboratory, Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China. Tel.: +86-20-38455491;
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13
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Rejali L, Seifollahi Asl R, Sanjabi F, Fatemi N, Asadzadeh Aghdaei H, Saeedi Niasar M, Ketabi Moghadam P, Nazemalhosseini Mojarad E, Mini E, Nobili S. Principles of Molecular Utility for CMS Classification in Colorectal Cancer Management. Cancers (Basel) 2023; 15:2746. [PMID: 37345083 DOI: 10.3390/cancers15102746] [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: 03/21/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Colorectal cancer (CRC) is the second cause of cancer-related deaths in both sexes globally and presents different clinical outcomes that are described by a range of genomic and epigenomic alterations. Despite the advancements in CRC screening plans and treatment strategies, the prognosis of CRC is dismal. In the last two decades, molecular biomarkers predictive of prognosis have been identified in CRC, although biomarkers predictive of treatment response are only available for specific biological drugs used in stage IV CRC. Translational clinical trials mainly based on "omic" strategies allowed a better understanding of the biological heterogeneity of CRCs. These studies were able to classify CRCs into subtypes mainly related to prognosis, recurrence risk, and, to some extent, also to treatment response. Accordingly, the comprehensive molecular characterizations of CRCs, including The Cancer Genome Atlas (TCGA) and consensus molecular subtype (CMS) classifications, were presented to improve the comprehension of the genomic and epigenomic landscapes of CRCs for a better patient management. The CMS classification obtained by the CRC subtyping consortium categorizes CRC into four consensus molecular subtypes (CMS1-4) characterized by different prognoses. In this review, we discussed the CMS classification in different settings with a focus on its relationships with precursor lesions, tumor immunophenotype, and gut microbiota, as well as on its role in predicting prognosis and/or response to pharmacological treatments, as a crucial step towards precision medicine.
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Affiliation(s)
- Leili Rejali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Romina Seifollahi Asl
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Fatemeh Sanjabi
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran P.O. Box 14496-14535, Iran
| | - Nayeralsadat Fatemi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Mahsa Saeedi Niasar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Pardis Ketabi Moghadam
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yaman Street, Chamran Expressway, Tehran P.O. Box 19857-17411, Iran
| | - Enrico Mini
- Department of Health Sciences, University of Florence, Viale Pieraccini, 6, 50139 Firenze, Italy
| | - Stefania Nobili
- Department of Neuroscience, Psychology, Drug Research and Child Health-NEUROFARBA-Pharmacology and Toxicology Section, University of Florence, Viale Pieraccini, 6, 50139 Firenze, Italy
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14
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Bordonaro M. Oncogenic and Receptor-Mediated Wnt Signaling Influence the Sensitivity of Colonic Cells to Butyrate. J Cancer 2023; 14:446-453. [PMID: 36860917 PMCID: PMC9969577 DOI: 10.7150/jca.82393] [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: 01/05/2023] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Deregulated Wnt signaling is responsible for most cases of colorectal cancer (CRC). Dietary fiber is protective against CRC and this activity is likely mediated by butyrate, a breakdown product of dietary fiber that hyperactivates Wnt signaling, repressing CRC proliferation and inducing apoptosis. Receptor-mediated Wnt signaling and oncogenic Wnt signaling, which is typically initiated by mutation in more downstream elements of the pathway, activate non-overlapping patterns of gene expression. Receptor-mediated signaling is associated with a poor prognosis for CRC while oncogenic signaling is associated with a relatively good prognosis. We have compared the expression of genes differentially expressed in receptor-mediated vs. oncogenic Wnt signaling to microarray data generated in our laboratory. Most importantly we evaluated these gene expression patterns comparing the early stage colon microadenoma line LT97 with the metastatic CRC cell line SW620. LT97 cells exhibit a gene expression pattern more strongly associated with that observed with oncogenic Wnt signaling, while SW620 cells exhibit a gene expression pattern moderately associated with that observed with receptor-mediated Wnt signaling. Given that SW620 cells are more advanced and malignant compared to LT97 cells, these findings are generally consistent with the better prognosis observed with tumors exhibiting a more oncogenic Wnt gene expression pattern. Importantly, LT97 cells are more sensitive to the effects of butyrate on proliferation and apoptosis that are CRC cells. We further examine these gene expression patterns in butyrate-resistant vs. butyrate-sensitive CRC cells. Based upon all of these observations, we hypothesize that colonic neoplastic cells exhibiting a more oncogenic as compared to receptor-mediated Wnt signaling gene expression pattern would be more sensitive to the effects of butyrate, and, hence, fiber, than are those cells exhibiting a more receptor-mediated Wnt signaling pattern of expression. Diet-derived butyrate may affect the differential patient outcomes resulting from the two types of Wnt signaling. We further posit that development of butyrate resistance and concomitant changes in Wnt signaling patterns, including associations with CBP and p300, disrupts the association between the two major types of Wnt signaling (receptor-mediated and oncogenic) and neoplastic progression/prognosis. Ideas about testing the hypothesis and therapeutic implications are briefly considered.
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Affiliation(s)
- Michael Bordonaro
- ✉ Corresponding author: Geisinger Commonwealth School of Medicine 525 Pine Street Scranton, PA 18509 Tel: 570-504-9646 Fax: 570-504-9636 ,
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15
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Meng H, Nan M, Li Y, Ding Y, Yin Y, Zhang M. Application of CRISPR-Cas9 gene editing technology in basic research, diagnosis and treatment of colon cancer. Front Endocrinol (Lausanne) 2023; 14:1148412. [PMID: 37020597 PMCID: PMC10067930 DOI: 10.3389/fendo.2023.1148412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/07/2023] [Indexed: 04/07/2023] Open
Abstract
Colon cancer is the fourth leading cause of cancer death worldwide, and its progression is accompanied by a complex array of genetic variations. CRISPR/Cas9 can identify new drug-resistant or sensitive mutations in colon cancer, and can use gene editing technology to develop new therapeutic targets and provide personalized treatments, thereby significantly improving the treatment of colon cancer patients. CRISPR/Cas9 systems are driving advances in biotechnology. RNA-directed Cas enzymes have accelerated the pace of basic research and led to clinical breakthroughs. This article reviews the rapid development of CRISPR/Cas in colon cancer, from gene editing to transcription regulation, gene knockout, genome-wide CRISPR tools, therapeutic targets, stem cell genomics, immunotherapy, metabolism-related genes and inflammatory bowel disease. In addition, the limitations and future development of CRISPR/Cas9 in colon cancer studies are reviewed. In conclusion, this article reviews the application of CRISPR-Cas9 gene editing technology in basic research, diagnosis and treatment of colon cancer.
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Affiliation(s)
- Hui Meng
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Mingzhi Zhang, ; Hui Meng,
| | - Manman Nan
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yizhen Li
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yi Ding
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuhui Yin
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Mingzhi Zhang
- Department of Oncology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Mingzhi Zhang, ; Hui Meng,
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16
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Lin SC, Haga K, Zeng XL, Estes MK. Generation of CRISPR-Cas9-mediated genetic knockout human intestinal tissue-derived enteroid lines by lentivirus transduction and single-cell cloning. Nat Protoc 2022; 17:1004-1027. [PMID: 35197604 PMCID: PMC9059808 DOI: 10.1038/s41596-021-00669-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022]
Abstract
Human intestinal tissue-derived enteroids (HIEs; also called organoids) are a powerful ex vivo model for gastrointestinal research. Genetic modification of these nontransformed cultures allows new insights into gene function and biological processes involved in intestinal diseases as well as gastrointestinal and donor segment-specific function. Here we provide a detailed technical pipeline and protocol for using the CRISPR-Cas9 genome editing system to knock out a gene of interest specifically in HIEs by lentiviral transduction and single-cell cloning. This protocol differs from a previously published alternative using electroporation of human colonoids to deliver piggyback transposons or CRISPR-Cas9 constructs, as this protocol uses a modified, fused LentiCRISPRv2-small-guiding RNA to express Cas9 and small-guiding RNA in a lentivirus. The protocol also includes the steps of gene delivery and subsequent single-cell cloning of the knockout cells as well as verification of clones and sequence identification of the mutation sites to establish knockout clones. An overview flowchart, step-by-step guidelines and troubleshooting suggestions are provided to aid the researcher in obtaining the genetic knockout HIE line within 2-3 months. In this protocol, we further describe how to use HIEs as an ex vivo model to assess host restriction factors for viral replication (using human norovirus replication as an example) by knocking out host attachment factors or innate immunity genes. Other applications are discussed to broaden the utility of this system, for example, to generate knockin or conditional knockout HIE lines to investigate the function of essential genes in many biological processes including other types of organoids.
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Affiliation(s)
- Shih-Ching Lin
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kei Haga
- Department of Infection Control and Immunology, Kitasato University, Tokyo, Japan
| | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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17
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Nicolas AM, Pesic M, Engel E, Ziegler PK, Diefenhardt M, Kennel KB, Buettner F, Conche C, Petrocelli V, Elwakeel E, Weigert A, Zinoveva A, Fleischmann M, Häupl B, Karakütük C, Bohnenberger H, Mosa MH, Kaderali L, Gaedcke J, Ghadimi M, Rödel F, Arkan MC, Oellerich T, Rödel C, Fokas E, Greten FR. Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer. Cancer Cell 2022; 40:168-184.e13. [PMID: 35120600 DOI: 10.1016/j.ccell.2022.01.004] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/12/2021] [Accepted: 01/11/2022] [Indexed: 12/14/2022]
Abstract
Standard cancer therapy targets tumor cells without considering possible damage on the tumor microenvironment that could impair therapy response. In rectal cancer patients we find that inflammatory cancer-associated fibroblasts (iCAFs) are associated with poor chemoradiotherapy response. Employing a murine rectal cancer model or patient-derived tumor organoids and primary stroma cells, we show that, upon irradiation, interleukin-1α (IL-1α) not only polarizes cancer-associated fibroblasts toward the inflammatory phenotype but also triggers oxidative DNA damage, thereby predisposing iCAFs to p53-mediated therapy-induced senescence, which in turn results in chemoradiotherapy resistance and disease progression. Consistently, IL-1 inhibition, prevention of iCAFs senescence, or senolytic therapy sensitizes mice to irradiation, while lower IL-1 receptor antagonist serum levels in rectal patients correlate with poor prognosis. Collectively, we unravel a critical role for iCAFs in rectal cancer therapy resistance and identify IL-1 signaling as an attractive target for stroma-repolarization and prevention of cancer-associated fibroblasts senescence.
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Affiliation(s)
- Adele M Nicolas
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Marina Pesic
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Esther Engel
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Department of Radiotherapy and Oncology, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Paul K Ziegler
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt/Main, Germany
| | - Markus Diefenhardt
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Department of Radiotherapy and Oncology, Goethe University Frankfurt, Frankfurt/Main, Germany; University Cancer Center Frankfurt Marburg (UCT), University Hospital Frankfurt, Frankfurt/Main, Germany
| | - Kilian B Kennel
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Florian Buettner
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Medicine, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Claire Conche
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Valentina Petrocelli
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Eiman Elwakeel
- Institute of Biochemistry I, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Andreas Weigert
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Institute of Biochemistry I, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Anna Zinoveva
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Maximilian Fleischmann
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Department of Radiotherapy and Oncology, Goethe University Frankfurt, Frankfurt/Main, Germany; University Cancer Center Frankfurt Marburg (UCT), University Hospital Frankfurt, Frankfurt/Main, Germany
| | - Björn Häupl
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Medicine, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Cem Karakütük
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | | | - Mohammed H Mosa
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Jochen Gaedcke
- Department of Surgery, University Medical Center, Göttingen, Germany
| | - Michael Ghadimi
- Department of Surgery, University Medical Center, Göttingen, Germany
| | - Franz Rödel
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Department of Radiotherapy and Oncology, Goethe University Frankfurt, Frankfurt/Main, Germany; University Cancer Center Frankfurt Marburg (UCT), University Hospital Frankfurt, Frankfurt/Main, Germany
| | - Melek C Arkan
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas Oellerich
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Medicine, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Claus Rödel
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Department of Radiotherapy and Oncology, Goethe University Frankfurt, Frankfurt/Main, Germany; University Cancer Center Frankfurt Marburg (UCT), University Hospital Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Emmanouil Fokas
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Department of Radiotherapy and Oncology, Goethe University Frankfurt, Frankfurt/Main, Germany; University Cancer Center Frankfurt Marburg (UCT), University Hospital Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Florian R Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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18
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Marinucci M, Ercan C, Taha-Mehlitz S, Fourie L, Panebianco F, Bianco G, Gallon J, Staubli S, Soysal SD, Zettl A, Rauthe S, Vosbeck J, Droeser RA, Bolli M, Peterli R, von Flüe M, Ng CKY, Kollmar O, Coto-Llerena M, Piscuoglio S. Standardizing Patient-Derived Organoid Generation Workflow to Avoid Microbial Contamination From Colorectal Cancer Tissues. Front Oncol 2022; 11:781833. [PMID: 35083141 PMCID: PMC8784867 DOI: 10.3389/fonc.2021.781833] [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: 09/23/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
The use of patient-derived organoids (PDO) as a valuable alternative to in vivo models significantly increased over the last years in cancer research. The ability of PDOs to genetically resemble tumor heterogeneity makes them a powerful tool for personalized drug screening. Despite the extensive optimization of protocols for the generation of PDOs from colorectal tissue, there is still a lack of standardization of tissue handling prior to processing, leading to microbial contamination of the organoid culture. Here, using a cohort of 16 patients diagnosed with colorectal carcinoma (CRC), we aimed to test the efficacy of phosphate-buffered saline (PBS), penicillin/streptomycin (P/S), and Primocin, alone or in combination, in preventing organoid cultures contamination when used in washing steps prior to tissue processing. Each CRC tissue was divided into 5 tissue pieces, and treated with each different washing solution, or none. After the washing steps, all samples were processed for organoid generation following the same standard protocol. We detected contamination in 62.5% of the non-washed samples, while the use of PBS or P/S-containing PBS reduced the contamination rate to 50% and 25%, respectively. Notably, none of the organoid cultures washed with PBS/Primocin-containing solution were contaminated. Interestingly, addition of P/S to the washing solution reduced the percentage of living cells compared to Primocin. Taken together, our results demonstrate that, prior to tissue processing, adding Primocin to the tissue washing solution is able to eliminate the risk of microbial contamination in PDO cultures, and that the use of P/S negatively impacts organoids growth. We believe that our easy-to-apply protocol might help increase the success rate of organoid generation from CRC patients.
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Affiliation(s)
- Mattia Marinucci
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Caner Ercan
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland.,Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Stephanie Taha-Mehlitz
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Basel, Switzerland
| | - Lana Fourie
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Basel, Switzerland
| | - Federica Panebianco
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Gaia Bianco
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - John Gallon
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sebastian Staubli
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Basel, Switzerland
| | - Savas D Soysal
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Basel, Switzerland
| | - Andreas Zettl
- Institute of Pathology, Viollier AG, Allschwil, Switzerland
| | - Stephan Rauthe
- Institute of Pathology, Viollier AG, Allschwil, Switzerland
| | - Jürg Vosbeck
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Raoul A Droeser
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Basel, Switzerland
| | - Martin Bolli
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Basel, Switzerland
| | - Ralph Peterli
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Basel, Switzerland
| | - Markus von Flüe
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Basel, Switzerland
| | - Charlotte K Y Ng
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Otto Kollmar
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Basel, Switzerland
| | - Mairene Coto-Llerena
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland.,Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Salvatore Piscuoglio
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland.,Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
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19
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Strategies for genetic manipulation of adult stem cell-derived organoids. Exp Mol Med 2021; 53:1483-1494. [PMID: 34663937 PMCID: PMC8569115 DOI: 10.1038/s12276-021-00609-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/21/2021] [Accepted: 03/05/2021] [Indexed: 01/08/2023] Open
Abstract
Organoid technology allows the expansion of primary epithelial cells from normal and diseased tissues, providing a unique model for human (patho)biology. In a three-dimensional environment, adult stem cells self-organize and differentiate to gain tissue-specific features. Accessibility to genetic manipulation enables the investigation of the molecular mechanisms underlying cell fate regulation, cell differentiation and cell interactions. In recent years, powerful methodologies using lentiviral transgenesis, CRISPR/Cas9 gene editing, and single-cell readouts have been developed to study gene function and carry out genetic screens in organoids. However, the multicellularity and dynamic nature of stem cell-derived organoids also present challenges for genetic experimentation. In this review, we focus on adult gastrointestinal organoids and summarize the state-of-the-art protocols for successful transgenesis. We provide an outlook on emerging genetic techniques that could further increase the applicability of organoids and enhance the potential of organoid-based techniques to deepen our understanding of gene function in tissue biology.
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20
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Guy B, Zhang JS, Duncan LH, Johnston RJ. Human neural organoids: Models for developmental neurobiology and disease. Dev Biol 2021; 478:102-121. [PMID: 34181916 PMCID: PMC8364509 DOI: 10.1016/j.ydbio.2021.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/08/2021] [Accepted: 06/24/2021] [Indexed: 12/25/2022]
Abstract
Human organoids stand at the forefront of basic and translational research, providing experimentally tractable systems to study human development and disease. These stem cell-derived, in vitro cultures can generate a multitude of tissue and organ types, including distinct brain regions and sensory systems. Neural organoid systems have provided fundamental insights into molecular mechanisms governing cell fate specification and neural circuit assembly and serve as promising tools for drug discovery and understanding disease pathogenesis. In this review, we discuss several human neural organoid systems, how they are generated, advances in 3D imaging and bioengineering, and the impact of organoid studies on our understanding of the human nervous system.
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Affiliation(s)
- Brian Guy
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
| | - Jingliang Simon Zhang
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
| | - Leighton H Duncan
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA.
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21
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Lewis-Israeli YR, Wasserman AH, Aguirre A. Heart Organoids and Engineered Heart Tissues: Novel Tools for Modeling Human Cardiac Biology and Disease. Biomolecules 2021; 11:1277. [PMID: 34572490 PMCID: PMC8468189 DOI: 10.3390/biom11091277] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/06/2021] [Accepted: 08/24/2021] [Indexed: 01/02/2023] Open
Abstract
Organoids are three-dimensional in vitro cell constructs that recapitulate organ properties and structure to a significant extent. They constitute particularly useful models to study unapproachable states in humans, such as embryonic and fetal development, or early disease progression in adults. In recent years organoids have been implemented to model a wide range of different organs and disease conditions. However, the technology for their fabrication and application to cardiovascular studies has been lagging significantly when compared to other organoid types (e.g., brain, pancreas, kidney, intestine). This is a surprising fact since cardiovascular disease (CVD) and congenital heart disease (CHD) constitute the leading cause of mortality and morbidity in the developed world, and the most common birth defect in humans, respectively, and collectively constitute one of the largest unmet medical needs in the modern world. There is a critical need to establish in vitro models of the human heart that faithfully recapitulate its biology and function, thus enabling basic and translational studies to develop new therapeutics. Generating heart organoids that truly resemble the heart has proven difficult due to its complexity, but significant progress has been made recently to overcome this obstacle. In this review, we will discuss progress in novel heart organoid generation methods, the advantages and disadvantages of each approach, and their translational applications for advancing cardiovascular studies and the treatment of heart disorders.
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Affiliation(s)
- Yonatan R. Lewis-Israeli
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48823, USA; (Y.R.L.-I.); (A.H.W.)
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI 48823, USA
| | - Aaron H. Wasserman
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48823, USA; (Y.R.L.-I.); (A.H.W.)
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI 48823, USA
| | - Aitor Aguirre
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48823, USA; (Y.R.L.-I.); (A.H.W.)
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI 48823, USA
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22
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Cho EJ, Kim M, Jo D, Kim J, Oh JH, Chung HC, Lee SH, Kim D, Chun SM, Kim J, Lee H, Kim TW, Yu CS, Sung CO, Jang SJ. Immuno-genomic classification of colorectal cancer organoids reveals cancer cells with intrinsic immunogenic properties associated with patient survival. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:230. [PMID: 34256801 PMCID: PMC8276416 DOI: 10.1186/s13046-021-02034-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/30/2021] [Indexed: 12/28/2022]
Abstract
Background The intrinsic immuno-ge7nomic characteristics of colorectal cancer cells that affect tumor biology and shape the tumor immune microenvironment (TIM) are unclear. Methods We developed a patient-derived colorectal cancer organoid (CCO) model and performed pairwise analysis of 87 CCOs and their matched primary tumors. The TIM type of the primary tumor was classified as immuno-active, immuno-exhausted, or immuno-desert. Results The gene expression profiles, signaling pathways, major oncogenic mutations, and histology of the CCOs recapitulated those of the primary tumors, but not the TIM of primary tumors. Two distinct intrinsic molecular subgroups of highly proliferative and mesenchymal phenotypes with clinical significance were identified in CCOs with various cancer signaling pathways. CCOs showed variable expression of cancer-specific immune-related genes such as those encoding HLA-I and HLA-II, and molecules involved in immune checkpoint activation/inhibition. Among these genes, the expression of HLA-II in CCOs was associated with favorable patient survival. K-means clustering analysis based on HLA-II expression in CCOs revealed a subgroup of patients, in whom cancer cells exhibited Intrinsically Immunogenic Properties (Ca-IIP), and were characterized by high expression of signatures associated with HLA-I, HLA-II, antigen presentation, and immune stimulation. Patients with the Ca-IIP phenotype had an excellent prognosis, irrespective of age, disease stage, intrinsic molecular type, or TIM status. Ca-IIP was negatively correlated with intrinsic E2F/MYC signaling. Analysis of the correlation between CCO immuno-genotype and TIM phenotype revealed that the TIM phenotype was associated with microsatellite instability, Wnt/β-catenin signaling, APC/KRAS mutations, and the unfolded protein response pathway linked to the FBXW7 mutation in cancer cells. However, Ca-IIP was not associated with the TIM phenotype. Conclusions We identified a Ca-IIP phenotype from a large set of CCOs. Our findings may provide an unprecedented opportunity to develop new strategies for optimal patient stratification in this era of immunotherapy. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02034-1.
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Affiliation(s)
- Eun Jeong Cho
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea.,Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Minsuh Kim
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Daum Jo
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Jihye Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Ji-Hye Oh
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea.,Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hee Chul Chung
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Sun-Hye Lee
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Deokhoon Kim
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea.,Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Sung-Min Chun
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea.,Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Jihun Kim
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea.,Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Hyeonjin Lee
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Tae Won Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Chang Sik Yu
- Department of Colon and Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Chang Ohk Sung
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea. .,Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea. .,Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea.
| | - Se Jin Jang
- Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea. .,Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea. .,Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea. .,OncoClew Life Science Co., Ltd, Songpa-gu, Seoul, Republic of Korea.
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23
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Ojo BA, VanDussen KL, Rosen MJ. The Promise of Patient-Derived Colon Organoids to Model Ulcerative Colitis. Inflamm Bowel Dis 2021; 28:299-308. [PMID: 34251431 PMCID: PMC8804507 DOI: 10.1093/ibd/izab161] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Indexed: 12/11/2022]
Abstract
Physiologic, molecular, and genetic findings all point to impaired intestinal epithelial function as a key element in the multifactorial pathogenesis of ulcerative colitis (UC). The lack of epithelial-directed therapies is a conspicuous weakness of our UC therapeutic armamentarium. However, a critical barrier to new drug discovery is the lack of preclinical human models of UC. Patient tissue-derived colon epithelial organoids (colonoids) are primary epithelial stem cell-derived in vitro structures capable of self-organization and self-renewal that hold great promise as a human preclinical model for UC drug development. Several single and multi-tissue systems for colonoid culture have been developed, including 3-dimensional colonoids grown in a gelatinous extracellular matrix, 2-dimensional polarized monolayers, and colonoids on a chip that model luminal and blood flow and nutrient delivery. A small number of pioneering studies suggest that colonoids derived from UC patients retain some disease-related transcriptional and epigenetic changes, but they also raise questions regarding the persistence of inflammatory transcriptional programs in culture over time. Additional research is needed to fully characterize the extent to which and under what conditions colonoids accurately model disease-associated epithelial molecular and functional aberrations. With further advancement and standardization of colonoid culture methodology, colonoids will likely become an important tool for realizing precision medicine in UC.
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Affiliation(s)
- Babajide A Ojo
- Divisions of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States
| | - Kelli L VanDussen
- Divisions of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States,Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
| | - Michael J Rosen
- Divisions of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States,Address correspondence to: Michael J. Rosen, MD, MSCI, Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 2010, Cincinnati, Ohio, 45229, United States. E-mail:
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24
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Zhang Y, Huang S, Zhong W, Chen W, Yao B, Wang X. 3D organoids derived from the small intestine: An emerging tool for drug transport research. Acta Pharm Sin B 2021; 11:1697-1707. [PMID: 34386316 PMCID: PMC8343122 DOI: 10.1016/j.apsb.2020.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/29/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
Small intestine in vitro models play a crucial role in drug transport research. Although conventional 2D cell culture models, such as Caco-2 monolayer, possess many advantages, they should be interpreted with caution because they have relatively poor physiologically reproducible phenotypes and functions. With the development of 3D culture technology, pluripotent stem cells (PSCs) and adult somatic stem cells (ASCs) show remarkable self-organization characteristics, which leads to the development of intestinal organoids. Based on previous studies, this paper reviews the application of intestinal 3D organoids in drug transport mediated by P-glycoprotein (P-gp), breast cancer resistance protein (BCRP) and multidrug resistance protein 2 (MRP2). The advantages and limitations of this model are also discussed. Although there are still many challenges, intestinal 3D organoid model has the potential to be an excellent tool for drug transport research.
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Key Words
- 3D organoid
- ASCs, adult somatic stem cells
- BCRP, breast cancer resistance protein
- BMP, bone morphogenetic protein
- CDF, 5(6)-carboxy-2′,7′-dichlorofluorescein
- Caco-2 cell monolayer
- DDI, drug–drug interactions
- Drug transporter
- EGF, epidermal growth factor
- ER, efflux ratio
- ESCs, embryonic stem cells
- FGF, fibroblast growth factor
- Lgr5+, leucine-rich-repeat-containing G-protein-coupled receptor 5 positive
- MCT, monocarboxylate transporter protein
- MRP2, multidrug resistance protein 2
- NBD, nucleotide-binding domain
- OATP, organic anion transporting polypeptide
- OCT, organic cation transporter
- OCTN, carnitine/organic cation transporter
- P-glycoprotein
- P-gp, P-glycoprotein
- PEPT, peptide transporter protein
- PMAT, plasma membrane monoamine transporter
- PSCs, pluripotent stem cells
- Papp, apparent permeability coefficient
- Rh123, rhodamine 123
- SLC, solute carrier
- Small intestine
- TEER, transepithelial electrical resistance
- TMDs, transmembrane domains
- cMOAT, canalicular multispecific organic anion transporter
- iPSCs, induced pluripotent stem cells
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Affiliation(s)
- Yuanjin Zhang
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200051, China
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Shengbo Huang
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200051, China
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Weiguo Zhong
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200051, China
| | - Wenxia Chen
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200051, China
| | - Bingyi Yao
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200051, China
| | - Xin Wang
- Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai 200051, China
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- Corresponding author. Tel.: +86 21 2420 6564; fax: +86 21 5434 4922.
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25
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Organoids and Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13112657. [PMID: 34071313 PMCID: PMC8197877 DOI: 10.3390/cancers13112657] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
Organoids were first established as a three-dimensional cell culture system from mouse small intestine. Subsequent development has made organoids a key system to study many human physiological and pathological processes that affect a variety of tissues and organs. In particular, organoids are becoming very useful tools to dissect colorectal cancer (CRC) by allowing the circumvention of classical problems and limitations, such as the impossibility of long-term culture of normal intestinal epithelial cells and the lack of good animal models for CRC. In this review, we describe the features and current knowledge of intestinal organoids and how they are largely contributing to our better understanding of intestinal cell biology and CRC genetics. Moreover, recent data show that organoids are appropriate systems for antitumoral drug testing and for the personalized treatment of CRC patients.
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26
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Hendriks D, Clevers H, Artegiani B. CRISPR-Cas Tools and Their Application in Genetic Engineering of Human Stem Cells and Organoids. Cell Stem Cell 2021; 27:705-731. [PMID: 33157047 DOI: 10.1016/j.stem.2020.10.014] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CRISPR-Cas technology has revolutionized biological research and holds great therapeutic potential. Here, we review CRISPR-Cas systems and their latest developments with an emphasis on application to human cells. We also discuss how different CRISPR-based strategies can be used to accomplish a particular genome engineering goal. We then review how different CRISPR tools have been used in genome engineering of human stem cells in vitro, covering both the pluripotent (iPSC/ESC) and somatic adult stem cell fields and, in particular, 3D organoid cultures. Finally, we discuss the progress and challenges associated with CRISPR-based genome editing of human stem cells for therapeutic use.
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Affiliation(s)
- Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; The Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.
| | - Benedetta Artegiani
- The Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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27
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Heuberger J, Trimpert J, Vladimirova D, Goosmann C, Lin M, Schmuck R, Mollenkopf H, Brinkmann V, Tacke F, Osterrieder N, Sigal M. Epithelial response to IFN-γ promotes SARS-CoV-2 infection. EMBO Mol Med 2021; 13:e13191. [PMID: 33544398 PMCID: PMC7995094 DOI: 10.15252/emmm.202013191] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2, the agent that causes COVID-19, invades epithelial cells, including those of the respiratory and gastrointestinal mucosa, using angiotensin-converting enzyme-2 (ACE2) as a receptor. Subsequent inflammation can promote rapid virus clearance, but severe cases of COVID-19 are characterized by an inefficient immune response that fails to clear the infection. Using primary epithelial organoids from human colon, we explored how the central antiviral mediator IFN-γ, which is elevated in COVID-19, affects epithelial cell differentiation, ACE2 expression, and susceptibility to infection with SARS-CoV-2. In mouse and human colon, ACE2 is mainly expressed by surface enterocytes. Inducing enterocyte differentiation in organoid culture resulted in increased ACE2 production. IFN-γ treatment promoted differentiation into mature KRT20+ enterocytes expressing high levels of ACE2, increased susceptibility to SARS-CoV-2 infection, and resulted in enhanced virus production in infected cells. Similarly, infection-induced epithelial interferon signaling promoted enterocyte maturation and enhanced ACE2 expression. We here reveal a mechanism by which IFN-γ-driven inflammatory responses induce a vulnerable epithelial state with robust replication of SARS-CoV-2, which may have an impact on disease outcome and virus transmission.
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Affiliation(s)
- Julian Heuberger
- Department of Hepatology and GastroenterologyCharité University MedicineBerlinGermany
- Department of Molecular BiologyMax Planck Institute for Infection BiologyBerlinGermany
- Berlin Institute for Medical Systems BiologyMax Delbrück Center for Molecular MedicineBerlinGermany
| | - Jakob Trimpert
- Institute of VirologyFreie Universität BerlinBerlinGermany
| | | | - Christian Goosmann
- Department of Molecular BiologyMax Planck Institute for Infection BiologyBerlinGermany
| | - Manqiang Lin
- Department of Hepatology and GastroenterologyCharité University MedicineBerlinGermany
| | - Rosa Schmuck
- Department of SurgeryCharité University MedicineBerlinGermany
| | | | - Volker Brinkmann
- Department of Molecular BiologyMax Planck Institute for Infection BiologyBerlinGermany
| | - Frank Tacke
- Department of Hepatology and GastroenterologyCharité University MedicineBerlinGermany
| | - Nikolaus Osterrieder
- Institute of VirologyFreie Universität BerlinBerlinGermany
- Department of Infectious Disease and Public HealthJockey Club College of Veterinary Medicine and Life SciencesCity University of Hong KongKowloonHong Kong
| | - Michael Sigal
- Department of Hepatology and GastroenterologyCharité University MedicineBerlinGermany
- Department of Molecular BiologyMax Planck Institute for Infection BiologyBerlinGermany
- Berlin Institute for Medical Systems BiologyMax Delbrück Center for Molecular MedicineBerlinGermany
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28
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Olesch C, Sirait-Fischer E, Berkefeld M, Fink AF, Susen RM, Ritter B, Michels BE, Steinhilber D, Greten FR, Savai R, Takeda K, Brüne B, Weigert A. S1PR4 ablation reduces tumor growth and improves chemotherapy via CD8+ T cell expansion. J Clin Invest 2021; 130:5461-5476. [PMID: 32663191 DOI: 10.1172/jci136928] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022] Open
Abstract
Tumor immunosuppression is a limiting factor for successful cancer therapy. The lipid sphingosine-1-phosphate (S1P), which signals through 5 distinct G protein-coupled receptors (S1PR1-5), has emerged as an important regulator of carcinogenesis. However, the utility of targeting S1P in tumors is hindered by S1P's impact on immune cell trafficking. Here, we report that ablation of the immune cell-specific receptor S1PR4, which plays a minor role in immune cell trafficking, delayed tumor development and improved therapy success in murine models of mammary and colitis-associated colorectal cancer through increased CD8+ T cell abundance. Transcriptome analysis revealed that S1PR4 affected proliferation and survival of CD8+ T cells in a cell-intrinsic manner via the expression of Pik3ap1 and Lta4h. Accordingly, PIK3AP1 expression was connected to increased CD8+ T cell proliferation and clinical parameters in human breast and colon cancer. Our data indicate a so-far-unappreciated tumor-promoting role of S1P by restricting CD8+ T cell expansion via S1PR4.
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Affiliation(s)
- Catherine Olesch
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Evelyn Sirait-Fischer
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Matthias Berkefeld
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Annika F Fink
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Rosa M Susen
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Birgit Ritter
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Germany.,Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany
| | - Birgitta E Michels
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Germany.,Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany.,German Cancer Consortium (DKTK), partner site Frankfurt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Florian R Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Germany.,Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany.,German Cancer Consortium (DKTK), partner site Frankfurt, Germany
| | - Rajkumar Savai
- Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany.,Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL) and the Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.,Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
| | - Kazuhiko Takeda
- Research Center of Oncology, ONO Pharmaceutical Co., Ltd., Osaka, Japan
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany.,Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany.,German Cancer Consortium (DKTK), partner site Frankfurt, Germany.,Branch for Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Frankfurt, Germany
| | - Andreas Weigert
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany.,Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany.,German Cancer Consortium (DKTK), partner site Frankfurt, Germany
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Bischoff NS, de Kok TM, Sijm DT, van Breda SG, Briedé JJ, Castenmiller JJ, Opperhuizen A, Chirino YI, Dirven H, Gott D, Houdeau E, Oomen AG, Poulsen M, Rogler G, van Loveren H. Possible Adverse Effects of Food Additive E171 (Titanium Dioxide) Related to Particle Specific Human Toxicity, Including the Immune System. Int J Mol Sci 2020; 22:ijms22010207. [PMID: 33379217 PMCID: PMC7795714 DOI: 10.3390/ijms22010207] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 12/12/2022] Open
Abstract
Titanium dioxide (TiO2) is used as a food additive (E171) and can be found in sauces, icings, and chewing gums, as well as in personal care products such as toothpaste and pharmaceutical tablets. Along with the ubiquitous presence of TiO2 and recent insights into its potentially hazardous properties, there are concerns about its application in commercially available products. Especially the nano-sized particle fraction (<100 nm) of TiO2 warrants a more detailed evaluation of potential adverse health effects after ingestion. A workshop organized by the Dutch Office for Risk Assessment and Research (BuRO) identified uncertainties and knowledge gaps regarding the gastrointestinal absorption of TiO2, its distribution, the potential for accumulation, and induction of adverse health effects such as inflammation, DNA damage, and tumor promotion. This review aims to identify and evaluate recent toxicological studies on food-grade TiO2 and nano-sized TiO2 in ex-vivo, in-vitro, and in-vivo experiments along the gastrointestinal route, and to postulate an Adverse Outcome Pathway (AOP) following ingestion. Additionally, this review summarizes recommendations and outcomes of the expert meeting held by the BuRO in 2018, in order to contribute to the hazard identification and risk assessment process of ingested TiO2.
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Affiliation(s)
- Nicolaj S. Bischoff
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (T.M.d.K.); (D.T.H.M.S.); (S.G.v.B.); (J.J.B.)
- Correspondence:
| | - Theo M. de Kok
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (T.M.d.K.); (D.T.H.M.S.); (S.G.v.B.); (J.J.B.)
| | - Dick T.H.M. Sijm
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (T.M.d.K.); (D.T.H.M.S.); (S.G.v.B.); (J.J.B.)
- Netherlands Food and Consumer Product Safety Authority, P.O. Box 43006, 3540 AA Utrecht, The Netherlands; (J.J.M.C.); (A.O.); (H.v.L.)
| | - Simone G. van Breda
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (T.M.d.K.); (D.T.H.M.S.); (S.G.v.B.); (J.J.B.)
| | - Jacco J. Briedé
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (T.M.d.K.); (D.T.H.M.S.); (S.G.v.B.); (J.J.B.)
| | - Jacqueline J.M. Castenmiller
- Netherlands Food and Consumer Product Safety Authority, P.O. Box 43006, 3540 AA Utrecht, The Netherlands; (J.J.M.C.); (A.O.); (H.v.L.)
| | - Antoon Opperhuizen
- Netherlands Food and Consumer Product Safety Authority, P.O. Box 43006, 3540 AA Utrecht, The Netherlands; (J.J.M.C.); (A.O.); (H.v.L.)
| | - Yolanda I. Chirino
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonóma de México, Mexico City 54090, Mexico;
| | - Hubert Dirven
- Norwegian Institute of Public Health, P.O. Box 222 Skøyen, 0213 Oslo, Norway;
| | - David Gott
- Food Standard Agency, London SW1H9EX, UK;
| | - Eric Houdeau
- French National Research Institute for Agriculture, Food and Environment (INRAE), 75338 Paris, France;
| | - Agnes G. Oomen
- National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, The Netherlands;
| | - Morten Poulsen
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark;
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital of Zurich, 8091 Zurich, Switzerland;
| | - Henk van Loveren
- Netherlands Food and Consumer Product Safety Authority, P.O. Box 43006, 3540 AA Utrecht, The Netherlands; (J.J.M.C.); (A.O.); (H.v.L.)
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Lindhorst PH, Hummon AB. Proteomics of Colorectal Cancer: Tumors, Organoids, and Cell Cultures-A Minireview. Front Mol Biosci 2020; 7:604492. [PMID: 33363210 PMCID: PMC7758474 DOI: 10.3389/fmolb.2020.604492] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/20/2020] [Indexed: 12/14/2022] Open
Abstract
Proteomics, the study of the complete protein composition of a sample, is an important field for cancer research. Changes in the proteome can serve as a biomarker of cancer or lead to the development of a targeted therapy. This minireview will focus on mass spectrometry-based proteomics studies applied specifically to colorectal cancer, particularly the variety of cancer model systems used, including tumor samples, two-dimensional (2D) and three-dimensional (3D) cell cultures such as spheroids and organoids. A thorough discussion of the application of these systems will accompany the review of the literature, as each provides distinct advantages and disadvantages for colorectal cancer research. Finally, we provide conclusions and future perspectives for the application of these model systems to cancer research as a whole.
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Affiliation(s)
- Philip H Lindhorst
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States.,The Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
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31
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Mosa MH, Michels BE, Menche C, Nicolas AM, Darvishi T, Greten FR, Farin HF. A Wnt-Induced Phenotypic Switch in Cancer-Associated Fibroblasts Inhibits EMT in Colorectal Cancer. Cancer Res 2020; 80:5569-5582. [PMID: 33055221 DOI: 10.1158/0008-5472.can-20-0263] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 08/19/2020] [Accepted: 10/09/2020] [Indexed: 11/16/2022]
Abstract
Tumor progression is recognized as a result of an evolving cross-talk between tumor cells and their surrounding nontransformed stroma. Although Wnt signaling has been intensively studied in colorectal cancer, it remains unclear whether activity in the tumor-associated stroma contributes to malignancy. To specifically interfere with stromal signals, we generated Wnt-independent tumor organoids that secrete the Wnt antagonist Sfrp1. Subcutaneous transplantation into immunocompetent as well as immunodeficient mice resulted in a strong reduction of tumor growth. Histologic and transcriptomic analyses revealed that Sfrp1 induced an epithelial-mesenchymal transition (EMT) phenotype in tumor cells without affecting tumor-intrinsic Wnt signaling, suggesting involvement of nonimmune stromal cells. Blockage of canonical signaling using Sfrp1, Dkk1, or fibroblast-specific genetic ablation of β-catenin strongly decreased the number of cancer-associated myofibroblasts (myCAF). Wnt activity in CAFs was linked with distinct subtypes, where low and high levels induced an inflammatory-like CAF (iCAF) subtype or contractile myCAFs, respectively. Coculture of tumor organoids with iCAFs resulted in significant upregulation of EMT markers, while myCAFs reverted this phenotype. In summary, we show that tumor growth and malignancy are differentially regulated via distinct fibroblast subtypes under the influence of juxtacrine Wnt signals. SIGNIFICANCE: This study provides evidence for Wnt-induced functional diversity of colorectal cancer-associated fibroblasts, representing a non-cell autonomous mechanism for colon cancer progression. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/24/5569/F1.large.jpg.
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Affiliation(s)
- Mohammed H Mosa
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Birgitta E Michels
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Constantin Menche
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Adele M Nicolas
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Tahmineh Darvishi
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Florian R Greten
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Henner F Farin
- German Cancer Consortium (DKTK), Heidelberg, Germany. .,Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
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Driehuis E, Kretzschmar K, Clevers H. Establishment of patient-derived cancer organoids for drug-screening applications. Nat Protoc 2020; 15:3380-3409. [PMID: 32929210 DOI: 10.1038/s41596-020-0379-4] [Citation(s) in RCA: 281] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 06/23/2020] [Indexed: 12/25/2022]
Abstract
Adult stem cell-based organoid technology is a versatile tool for the generation and long-term maintenance of near-native 3D epithelial tissues in vitro. The generation of cancer organoids from primary patient material enables a range of therapeutic agents to be tested in the resulting organoid cultures. Patient-derived cancer organoids therefore hold great promise for personalized medicine. Here, we provide an overview of the protocols used by different groups to establish organoids from various epithelial tissues and cancers, plus the different protocols subsequently used to test the in vitro therapy sensitivity of these patient-derived organoids. We also provide an in-depth protocol for the generation of head and neck squamous cell carcinoma organoids and their subsequent use in semi-automated therapy screens. Establishment of organoids and subsequent screening can be performed within 3 months, although this timeline is highly dependent on a.o. starting material and the number of therapies tested. The protocol provided may serve as a reference to successfully establish organoids from other cancer types and perform drug screenings thereof.
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Affiliation(s)
- Else Driehuis
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Utrecht, the Netherlands
- Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
- Department of Pathology, University Medical Center (UMC) Utrecht, Utrecht, the Netherlands
| | - Kai Kretzschmar
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Utrecht, the Netherlands.
- Mildred-Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, Würzburg, Germany.
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Utrecht, the Netherlands.
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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Dunbar K, Valanciute A, Lima ACS, Vinuela PF, Jamieson T, Rajasekaran V, Blackmur J, Ochocka-Fox AM, Guazzelli A, Cammareri P, Arends MJ, Sansom OJ, Myant KB, Farrington SM, Dunlop MG, Din FVN. Aspirin Rescues Wnt-Driven Stem-like Phenotype in Human Intestinal Organoids and Increases the Wnt Antagonist Dickkopf-1. Cell Mol Gastroenterol Hepatol 2020; 11:465-489. [PMID: 32971322 PMCID: PMC7797380 DOI: 10.1016/j.jcmgh.2020.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND & AIMS Aspirin reduces colorectal cancer (CRC) incidence and mortality. Understanding the biology responsible for this protective effect is key to developing biomarker-led approaches for rational clinical use. Wnt signaling drives CRC development from initiation to progression through regulation of epithelial-mesenchymal transition (EMT) and cancer stem cell populations. Here, we investigated whether aspirin can rescue these proinvasive phenotypes associated with CRC progression in Wnt-driven human and mouse intestinal organoids. METHODS We evaluated aspirin-mediated effects on phenotype and stem cell markers in intestinal organoids derived from mouse (ApcMin/+ and Apcflox/flox) and human familial adenomatous polyposis patients. CRC cell lines (HCT116 and Colo205) were used to study effects on motility, invasion, Wnt signaling, and EMT. RESULTS Aspirin rescues the Wnt-driven cystic organoid phenotype by promoting budding in mouse and human Apc deficient organoids, which is paralleled by decreased stem cell marker expression. Aspirin-mediated Wnt inhibition in ApcMin/+ mice is associated with EMT inhibition and decreased cell migration, invasion, and motility in CRC cell lines. Chemical Wnt activation induces EMT and stem-like alterations in CRC cells, which are rescued by aspirin. Aspirin increases expression of the Wnt antagonist Dickkopf-1 in CRC cells and organoids derived from familial adenomatous polyposis patients, which contributes to EMT and cancer stem cell inhibition. CONCLUSIONS We provide evidence of phenotypic biomarkers of response to aspirin with an increased epithelial and reduced stem-like state mediated by an increase in Dickkopf-1. This highlights a novel mechanism of aspirin-mediated Wnt inhibition and potential phenotypic and molecular biomarkers for trials.
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Affiliation(s)
- Karen Dunbar
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Asta Valanciute
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Ana Cristina Silva Lima
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Paz Freile Vinuela
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Thomas Jamieson
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Vidya Rajasekaran
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - James Blackmur
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Anna-Maria Ochocka-Fox
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Alice Guazzelli
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Patrizia Cammareri
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Mark J Arends
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom; Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kevin B Myant
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Susan M Farrington
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Malcolm G Dunlop
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Farhat V N Din
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom.
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Bian J, Dannappel M, Wan C, Firestein R. Transcriptional Regulation of Wnt/β-Catenin Pathway in Colorectal Cancer. Cells 2020; 9:cells9092125. [PMID: 32961708 PMCID: PMC7564852 DOI: 10.3390/cells9092125] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
The Wnt/β-catenin signaling pathway exerts integral roles in embryogenesis and adult homeostasis. Aberrant activation of the pathway is implicated in growth-associated diseases and cancers, especially as a key driver in the initiation and progression of colorectal cancer (CRC). Loss or inactivation of Adenomatous polyposis coli (APC) results in constitutive activation of Wnt/β-catenin signaling, which is considered as an initiating event in the development of CRC. Increased Wnt/β-catenin signaling is observed in virtually all CRC patients, underscoring the importance of this pathway for therapeutic intervention. Prior studies have deciphered the regulatory networks required for the cytoplasmic stabilisation or degradation of the Wnt pathway effector, β-catenin. However, the mechanism whereby nuclear β-catenin drives or inhibits expression of Wnt target genes is more diverse and less well characterised. Here, we describe a brief synopsis of the core canonical Wnt pathway components, set the spotlight on nuclear mediators and highlight the emerging role of chromatin regulators as modulators of β-catenin-dependent transcription activity and oncogenic output.
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Affiliation(s)
- Jia Bian
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; (J.B.); (M.D.); (C.W.)
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3800, Australia
| | - Marius Dannappel
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; (J.B.); (M.D.); (C.W.)
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3800, Australia
| | - Chunhua Wan
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; (J.B.); (M.D.); (C.W.)
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3800, Australia
| | - Ron Firestein
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; (J.B.); (M.D.); (C.W.)
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3800, Australia
- Correspondence:
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Costales-Carrera A, Fernández-Barral A, Bustamante-Madrid P, Domínguez O, Guerra-Pastrián L, Cantero R, del Peso L, Burgos A, Barbáchano A, Muñoz A. Comparative Study of Organoids from Patient-Derived Normal and Tumor Colon and Rectal Tissue. Cancers (Basel) 2020; 12:cancers12082302. [PMID: 32824266 PMCID: PMC7465167 DOI: 10.3390/cancers12082302] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Colon and rectal tumors, often referred to as colorectal cancer, show different gene expression patterns in studies that analyze whole tissue biopsies containing a mix of tumor and non-tumor cells. To better characterize colon and rectal tumors, we investigated the gene expression profile of organoids generated from endoscopic biopsies of rectal tumors and adjacent normal colon and rectum mucosa from therapy-naive rectal cancer patients. We also studied the effect of vitamin D on these organoid types. Gene profiling was performed by RNA-sequencing. Organoids from a normal colon and rectum had a shared gene expression profile that profoundly differed from that of rectal tumor organoids. We identified a group of genes of the biosynthetic machinery as rectal tumor organoid-specific, including those encoding the RNA polymerase II subunits POLR2H and POLR2J. The active vitamin D metabolite 1α,25-dihydroxyvitamin D3/calcitriol upregulated stemness-related genes (LGR5, LRIG1, SMOC2, and MSI1) in normal rectum organoids, while it downregulated differentiation marker genes (TFF2 and MUC2). Normal colon and rectum organoids share similar gene expression patterns and respond similarly to calcitriol. Rectal tumor organoids display distinct and heterogeneous gene expression profiles, with differences with respect to those of colon tumor organoids, and respond differently to calcitriol than normal rectum organoids.
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Affiliation(s)
- Alba Costales-Carrera
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (A.C.-C.); (A.F.-B.); (P.B.-M.); (L.d.P.); (A.B.)
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Centro de Investigaciones Biomédicas en Red-Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Asunción Fernández-Barral
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (A.C.-C.); (A.F.-B.); (P.B.-M.); (L.d.P.); (A.B.)
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Centro de Investigaciones Biomédicas en Red-Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Pilar Bustamante-Madrid
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (A.C.-C.); (A.F.-B.); (P.B.-M.); (L.d.P.); (A.B.)
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Centro de Investigaciones Biomédicas en Red-Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Orlando Domínguez
- Unidad de Genómica, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain;
| | - Laura Guerra-Pastrián
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Departamento de Patología, Hospital Universitario La Paz, 28029 Madrid, Spain
| | - Ramón Cantero
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Unidad Colorrectal, Departamento de Cirugía, Hospital Universitario La Paz, 28029 Madrid, Spain
| | - Luis del Peso
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (A.C.-C.); (A.F.-B.); (P.B.-M.); (L.d.P.); (A.B.)
- Centro de Investigaciones Biomédicas en Red-Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
| | - Aurora Burgos
- Unidad de Endoscopia, Departamento de Digestivo, Hospital Universitario La Paz, 28029 Madrid, Spain;
| | - Antonio Barbáchano
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (A.C.-C.); (A.F.-B.); (P.B.-M.); (L.d.P.); (A.B.)
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Centro de Investigaciones Biomédicas en Red-Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Alberto Muñoz
- Departamento de Biología del Cáncer, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (A.C.-C.); (A.F.-B.); (P.B.-M.); (L.d.P.); (A.B.)
- Instituto de Investigación del Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain; (L.G.-P.); (R.C.)
- Centro de Investigaciones Biomédicas en Red-Cáncer (CIBERONC), 28029 Madrid, Spain
- Correspondence:
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Shin W, Wu A, Min S, Shin YC, Fleming RYD, Eckhardt SG, Kim HJ. Spatiotemporal Gradient and Instability of Wnt Induce Heterogeneous Growth and Differentiation of Human Intestinal Organoids. iScience 2020; 23:101372. [PMID: 32745985 PMCID: PMC7398973 DOI: 10.1016/j.isci.2020.101372] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/22/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022] Open
Abstract
In a conventional culture of three-dimensional human intestinal organoids, extracellular matrix hydrogel has been used to provide a physical space for the growth and morphogenesis of organoids in the presence of exogenous morphogens such as Wnt3a. We found that organoids embedded in a dome-shaped hydrogel show significant size heterogeneity in different locations inside the hydrogel. Computational simulations revealed that the instability and diffusion limitation of Wnt3a constitutively generate a concentration gradient inside the hydrogel. The location-dependent heterogeneity of organoids in a hydrogel dome substantially perturbed the transcriptome profile associated with epithelial functions, cytodifferentiation including mucin 2 expression, and morphological characteristics. This heterogeneous phenotype was significantly mitigated when the Wnt3a was frequently replenished in the culture medium. Our finding suggests that the morphological, transcriptional, translational, and functional heterogeneity in conventional organoid cultures may lead to a false interpretation of the experimental results in organoid-based studies.
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Affiliation(s)
- Woojung Shin
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton St., Austin, TX 78712, USA
| | - Alexander Wu
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton St., Austin, TX 78712, USA
| | - Soyoun Min
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton St., Austin, TX 78712, USA
| | - Yong Cheol Shin
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton St., Austin, TX 78712, USA
| | - R Y Declan Fleming
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA; Department of Surgery and Perioperative Care, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - S Gail Eckhardt
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hyun Jung Kim
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton St., Austin, TX 78712, USA; Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA; Department of Medical Engineering, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.
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37
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Dietinger V, García de Durango CR, Wiechmann S, Boos SL, Michl M, Neumann J, Hermeking H, Kuster B, Jung P. Wnt-driven LARGE2 mediates laminin-adhesive O-glycosylation in human colonic epithelial cells and colorectal cancer. Cell Commun Signal 2020; 18:102. [PMID: 32586342 PMCID: PMC7315491 DOI: 10.1186/s12964-020-00561-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/23/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Wnt signaling drives epithelial self-renewal and disease progression in human colonic epithelium and colorectal cancer (CRC). Characterization of Wnt effector pathways is key for our understanding of these processes and for developing therapeutic strategies that aim to preserve tissue homeostasis. O-glycosylated cell surface proteins, such as α-dystroglycan (α-DG), mediate cellular adhesion to extracellular matrix components. We revealed a Wnt/LARGE2/α-DG signaling pathway which triggers this mode of colonic epithelial cell-to-matrix interaction in health and disease. METHODS Next generation sequencing upon shRNA-mediated silencing of adenomatous polyposis coli (APC), and quantitative chromatin immunoprecipitation (qChIP) combined with CRISPR/Cas9-mediated transcription factor binding site targeting characterized LARGE2 as a Wnt target gene. Quantitative mass spectrometry analysis on size-fractionated, glycoprotein-enriched samples revealed functional O-glycosylation of α-DG by LARGE2 in CRC. The biology of Wnt/LARGE2/α-DG signaling was assessed by affinity-based glycoprotein enrichment, laminin overlay, CRC-to-endothelial cell adhesion, and transwell migration assays. Experiments on primary tissue, human colonic (tumor) organoids, and bioinformatic analysis of CRC cohort data confirmed the biological relevance of our findings. RESULTS Next generation sequencing identified the LARGE2 O-glycosyltransferase encoding gene as differentially expressed upon Wnt activation in CRC. Silencing of APC, conditional expression of oncogenic β-catenin and endogenous β-catenin-sequestration affected LARGE2 expression. The first intron of LARGE2 contained a CTTTGATC motif essential for Wnt-driven LARGE2 expression, showed occupation by the Wnt transcription factor TCF7L2, and Wnt activation triggered LARGE2-dependent α-DG O-glycosylation and laminin-adhesion in CRC cells. Colonic crypts and organoids expressed LARGE2 mainly in stem cell-enriched subpopulations. In human adenoma organoids, activity of the LARGE2/α-DG axis was Wnt-dose dependent. LARGE2 expression was elevated in CRC and correlated with the Wnt-driven molecular subtype and intestinal stem cell features. O-glycosylated α-DG represented a Wnt/LARGE2-dependent feature in CRC cell lines and patient-derived tumor organoids. Modulation of LARGE2/α-DG signaling affected CRC cell migration through laminin-coated membranes and adhesion to endothelial cells. CONCLUSIONS We conclude that the LARGE2 O-glycosyltransferase-encoding gene represents a direct target of canonical Wnt signaling and mediates functional O-glycosylation of α-dystroglycan (α-DG) in human colonic stem/progenitor cells and Wnt-driven CRC. Our work implies that aberrant Wnt activation augments CRC cell-matrix adhesion by increasing LARGE/α-DG-mediated laminin-adhesiveness. Video abstract.
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Affiliation(s)
- Vanessa Dietinger
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany.,DKTK Research Group, Oncogenic Signaling Pathways of Colorectal Cancer, Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Cira R García de Durango
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany.,DKTK Research Group, Oncogenic Signaling Pathways of Colorectal Cancer, Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Svenja Wiechmann
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany.,Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Sophie L Boos
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany.,DKTK Research Group, Oncogenic Signaling Pathways of Colorectal Cancer, Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marlies Michl
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jens Neumann
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Heiko Hermeking
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany.,Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Bernhard Kuster
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany.,Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| | - Peter Jung
- German Cancer Research Center (DKFZ), Heidelberg, Germany. .,German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany. .,DKTK Research Group, Oncogenic Signaling Pathways of Colorectal Cancer, Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany. .,DKTK AG Oncogenic Signal Transduction Pathways in Colorectal/Pancreatic Cancer, Deutsches Krebsforschungszentrum (DKFZ) Heidelberg, DKTK Partnerstandort München, Institut für Pathologie der Ludwig-Maximilians-Universität (LMU) München, Thalkirchner Straße 36, D-80337, Munich, Germany.
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38
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Cassotta M, Forbes-Hernández TY, Calderón Iglesias R, Ruiz R, Elexpuru Zabaleta M, Giampieri F, Battino M. Links between Nutrition, Infectious Diseases, and Microbiota: Emerging Technologies and Opportunities for Human-Focused Research. Nutrients 2020; 12:E1827. [PMID: 32575399 PMCID: PMC7353391 DOI: 10.3390/nu12061827] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 02/06/2023] Open
Abstract
The interaction between nutrition and human infectious diseases has always been recognized. With the emergence of molecular tools and post-genomics, high-resolution sequencing technologies, the gut microbiota has been emerging as a key moderator in the complex interplay between nutrients, human body, and infections. Much of the host-microbial and nutrition research is currently based on animals or simplistic in vitro models. Although traditional in vivo and in vitro models have helped to develop mechanistic hypotheses and assess the causality of the host-microbiota interactions, they often fail to faithfully recapitulate the complexity of the human nutrient-microbiome axis in gastrointestinal homeostasis and infections. Over the last decade, remarkable progress in tissue engineering, stem cell biology, microfluidics, sequencing technologies, and computing power has taken place, which has produced a new generation of human-focused, relevant, and predictive tools. These tools, which include patient-derived organoids, organs-on-a-chip, computational analyses, and models, together with multi-omics readouts, represent novel and exciting equipment to advance the research into microbiota, infectious diseases, and nutrition from a human-biology-based perspective. After considering some limitations of the conventional in vivo and in vitro approaches, in this review, we present the main novel available and emerging tools that are suitable for designing human-oriented research.
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Affiliation(s)
- Manuela Cassotta
- Centre for Nutrition and Health, Universidad Europea del Atlántico (UEA), 39001 Santander, Spain; (M.C.); (R.C.I.); (R.R.)
| | - Tamara Yuliett Forbes-Hernández
- Department of Analytical and Food Chemistry, Nutrition and Food Science Group, CITACA, CACTI, University of Vigo, 36310 Vigo, Spain;
| | - Ruben Calderón Iglesias
- Centre for Nutrition and Health, Universidad Europea del Atlántico (UEA), 39001 Santander, Spain; (M.C.); (R.C.I.); (R.R.)
| | - Roberto Ruiz
- Centre for Nutrition and Health, Universidad Europea del Atlántico (UEA), 39001 Santander, Spain; (M.C.); (R.C.I.); (R.R.)
| | - Maria Elexpuru Zabaleta
- Dipartimento di Scienze Cliniche e Molecolari, Facoltà di Medicina, Università Politecnica delle Marche, 60131 Ancona, Italy;
| | - Francesca Giampieri
- Department of Analytical and Food Chemistry, Nutrition and Food Science Group, CITACA, CACTI, University of Vigo, 36310 Vigo, Spain;
- Department of Clinical Sciences, Faculty of Medicine, Polytechnic University of Marche, 60131 Ancona, Italy
- College of Food Science and Technology, Northwest University, Xi’an 710069, China
| | - Maurizio Battino
- Department of Analytical and Food Chemistry, Nutrition and Food Science Group, CITACA, CACTI, University of Vigo, 36310 Vigo, Spain;
- Department of Clinical Sciences, Faculty of Medicine, Polytechnic University of Marche, 60131 Ancona, Italy
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
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39
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Bhattacharya S, Calar K, de la Puente P. Mimicking tumor hypoxia and tumor-immune interactions employing three-dimensional in vitro models. J Exp Clin Cancer Res 2020; 39:75. [PMID: 32357910 PMCID: PMC7195738 DOI: 10.1186/s13046-020-01583-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/22/2020] [Indexed: 02/06/2023] Open
Abstract
The heterogeneous tumor microenvironment (TME) is highly complex and not entirely understood. These complex configurations lead to the generation of oxygen-deprived conditions within the tumor niche, which modulate several intrinsic TME elements to promote immunosuppressive outcomes. Decoding these communications is necessary for designing effective therapeutic strategies that can effectively reduce tumor-associated chemotherapy resistance by employing the inherent potential of the immune system.While classic two-dimensional in vitro research models reveal critical hypoxia-driven biochemical cues, three-dimensional (3D) cell culture models more accurately replicate the TME-immune manifestations. In this study, we review various 3D cell culture models currently being utilized to foster an oxygen-deprived TME, those that assess the dynamics associated with TME-immune cell penetrability within the tumor-like spatial structure, and discuss state of the art 3D systems that attempt recreating hypoxia-driven TME-immune outcomes. We also highlight the importance of integrating various hallmarks, which collectively might influence the functionality of these 3D models.This review strives to supplement perspectives to the quickly-evolving discipline that endeavors to mimic tumor hypoxia and tumor-immune interactions using 3D in vitro models.
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Affiliation(s)
- Somshuvra Bhattacharya
- Cancer Biology and Immunotherapies Group, Sanford Research, 2301 E 60th Street N, Sioux Falls, SD, 57104, USA
| | - Kristin Calar
- Cancer Biology and Immunotherapies Group, Sanford Research, 2301 E 60th Street N, Sioux Falls, SD, 57104, USA
| | - Pilar de la Puente
- Cancer Biology and Immunotherapies Group, Sanford Research, 2301 E 60th Street N, Sioux Falls, SD, 57104, USA.
- Department of Surgery, University of South Dakota Sanford School of Medicine, Sioux Falls, SD, USA.
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD, USA.
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40
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Jackstadt R, Hodder MC, Sansom OJ. WNT and β-Catenin in Cancer: Genes and Therapy. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2020. [DOI: 10.1146/annurev-cancerbio-030419-033628] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The WNT pathway is a pleiotropic signaling pathway that controls developmental processes, tissue homeostasis, and cancer. The WNT pathway is commonly mutated in many cancers, leading to widespread research into the role of WNT signaling in carcinogenesis. Understanding which cancers are reliant upon WNT activation and which components of the WNT signaling pathway are mutated is paramount to advancing therapeutic strategies. In addition, building holistic insights into the role of WNT signaling in not only tumor cells but also the tumor microenvironment is a vital area of research and may be a promising therapeutic strategy in multiple immunologically inert cancers. Novel compounds aimed at modulating the WNT signaling pathway using diverse mechanisms are currently under investigation in preclinical/early clinical studies. Here, we review how the WNT pathway is activated in multiple cancers and discuss current strategies to target aberrant WNT signaling.
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Affiliation(s)
- Rene Jackstadt
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, United Kingdom
| | | | - Owen James Sansom
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, United Kingdom
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom
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41
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Human Gastrointestinal Organoid Models for Studying Microbial Disease and Cancer. Curr Top Microbiol Immunol 2020; 430:55-75. [PMID: 32889597 DOI: 10.1007/82_2020_223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
One of the major discoveries in stem cell research in the past decade embraces the development of "organs in a dish," also known as "organoids." Organoids are three-dimensional cellular structures derived from primary stem cells of different organ-specific cell types which are capable of self-renewal and maintenance of the parental lineages. Researchers have developed in vitro organoid models to mimic in vivo host-microbial interactions and disease. In this review, we focus on the use of gastrointestinal organoids as models of microbial disease and cancer.
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42
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Idris M, Harmston N, Petretto E, Madan B, Virshup DM. Broad regulation of gene isoform expression by Wnt signaling in cancer. RNA (NEW YORK, N.Y.) 2019; 25:1696-1713. [PMID: 31506381 PMCID: PMC6859862 DOI: 10.1261/rna.071506.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/06/2019] [Indexed: 05/08/2023]
Abstract
Differential gene isoform expression is a ubiquitous mechanism to enhance proteome diversity and maintain cell homeostasis. Mechanisms such as splicing that drive gene isoform variability are highly dynamic and responsive to changes in cell signaling pathways. Wnt/β-catenin signaling has profound effects on cell activity and cell fate and is known to modify several splicing events by altering the expression of individual splicing factors. However, a global assessment of how extensively Wnt signaling regulates splicing and other mechanisms that determine mRNA isoform composition in cancer is lacking. We used deep time-resolved RNA-seq in two independent in vivo Wnt-addicted tumor models during treatment with the potent Wnt inhibitor ETC-159 and examined Wnt regulated splicing events and splicing regulators. We found 1025 genes that underwent Wnt regulated variable exon usage leading to isoform expression changes. This was accompanied by extensive Wnt regulated changes in the expression of splicing regulators. Many of these Wnt regulated events were conserved in multiple human cancers, and many were linked to previously defined cancer-associated splicing quantitative trait loci. This suggests that the Wnt regulated splicing events are components of fundamental oncogenic processes. These findings demonstrate the wide-ranging effects of Wnt signaling on the isoform composition of the cell and provides an extensive resource of expression changes of splicing regulators and gene isoforms regulated by Wnt signaling.
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Affiliation(s)
- Muhammad Idris
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
| | - Nathan Harmston
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
- Centre for Computational Biology and Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857
- Science Division, Yale-NUS College, Singapore, 138527
| | - Enrico Petretto
- Centre for Computational Biology and Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857
| | - Babita Madan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
| | - David M Virshup
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina 27705, USA
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43
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Merenda A, Fenderico N, Maurice MM. Wnt Signaling in 3D: Recent Advances in the Applications of Intestinal Organoids. Trends Cell Biol 2019; 30:60-73. [PMID: 31718893 DOI: 10.1016/j.tcb.2019.10.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/14/2019] [Accepted: 10/14/2019] [Indexed: 02/06/2023]
Abstract
Intestinal organoids grown from adult stem cells have emerged as prototype 3D organotypic models for studying tissue renewal and homeostasis. Owing to their strict dependence on Wnt signaling, intestinal organoids offer an unprecedented opportunity to examine Wnt pathway regulation in normal physiology and cancer. We review how alterations in growth factor dependency and organoid morphology can be exploited to identify Wnt signaling mechanisms, characterize mutated pathway components, and predict responses of patient-derived tumors to targeted therapy. We discuss current deficits in the understanding of genotype-phenotype relationships that are to be considered when interpreting mutation-induced changes in organoid morphology.
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Affiliation(s)
- Alessandra Merenda
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, the Netherlands
| | - Nicola Fenderico
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, the Netherlands
| | - Madelon M Maurice
- Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, the Netherlands.
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44
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Flanagan DJ, Vincan E, Phesse TJ. Wnt Signaling in Cancer: Not a Binary ON:OFF Switch. Cancer Res 2019; 79:5901-5906. [PMID: 31431458 DOI: 10.1158/0008-5472.can-19-1362] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/16/2019] [Accepted: 08/07/2019] [Indexed: 11/16/2022]
Abstract
In the March 1 issue of Cancer Research, we identified the Wnt receptor Fzd7 as an attractive therapeutic target for the treatment of gastric cancer. In summary, we showed that pharmacological inhibition of Wnt receptors, or genetic deletion of Fzd7, blocks the initiation and growth of gastric tumors. Inhibiting Fzd receptors, specifically Fzd7, inhibits the growth of gastric cancer cells even in the presence of adenomatous polyposis coli (Apc) mutation. Apc is located in the cytoplasm downstream of Fzd7 in the Wnt signaling cascade and APC mutations activate Wnt/β-catenin signaling, therefore, this result seems counterintuitive. Here, we analyze this result in greater detail in the context of current knowledge of Wnt signaling and discuss the wider implications of this aspect of Wnt signaling in other cancers.
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Affiliation(s)
| | - Elizabeth Vincan
- University of Melbourne and Victorian Infectious Diseases Reference Laboratory, Doherty Institute of Infection and Immunity, Melbourne, Australia. .,School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Australia
| | - Toby J Phesse
- European Cancer Stem Cell Research Institute, Cardiff University, Cardiff, United Kingdom. .,Doherty Institute of Infection and Immunity, Melbourne, Australia
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45
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Xia X, Li F, He J, Aji R, Gao D. Organoid technology in cancer precision medicine. Cancer Lett 2019; 457:20-27. [PMID: 31078736 DOI: 10.1016/j.canlet.2019.04.039] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/22/2019] [Accepted: 04/25/2019] [Indexed: 12/13/2022]
Abstract
Organoid technology has been remarkably improved over the last decade. Various organoids have been derived from different types of tissues and recapitulate their organ-specific gene expression signatures, particular tissue spatial structures and functions of their original tissue. The patient-derived organoids (PDOs) have been used to elucidate crucial scientific questions, including the relationships between genetic/epigenetic alterations and drug responses, cell plasticity during disease progressions, and mechanisms of drug resistances. With the great expectations, PDOs will be widely used to facilitate the personalized medical decisions, which have the potential to profoundly improve patient outcomes. In this review, we will discuss the developmental details, current achievements, applications and challenges of organoid technology in precision cancer medicine.
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Affiliation(s)
- Xinyi Xia
- State Key Laboratory of Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; CAS Key Laboratory of Systems Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Fei Li
- State Key Laboratory of Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; CAS Key Laboratory of Systems Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Juan He
- State Key Laboratory of Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; CAS Key Laboratory of Systems Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Rebiguli Aji
- State Key Laboratory of Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; CAS Key Laboratory of Systems Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Dong Gao
- State Key Laboratory of Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; CAS Key Laboratory of Systems Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
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