1
|
Ahmad Zawawi SS, Salleh EA, Musa M. Spheroids and organoids derived from colorectal cancer as tools for in vitro drug screening. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:409-431. [PMID: 38745769 PMCID: PMC11090692 DOI: 10.37349/etat.2024.00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/02/2024] [Indexed: 05/16/2024] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease. Conventional two-dimensional (2D) culture employing cell lines was developed to study the molecular properties of CRC in vitro. Although these cell lines which are isolated from the tumor niche in which cancer develop, the translation to human model such as studying drug response is often hindered by the inability of cell lines to recapture original tumor features and the lack of heterogeneous clinical tumors represented by this 2D model, differed from in vivo condition. These limitations which may be overcome by utilizing three-dimensional (3D) culture consisting of spheroids and organoids. Over the past decade, great advancements have been made in optimizing culture method to establish spheroids and organoids of solid tumors including of CRC for multiple purposes including drug screening and establishing personalized medicine. These structures have been proven to be versatile and robust models to study CRC progression and deciphering its heterogeneity. This review will describe on advances in 3D culture technology and the application as well as the challenges of CRC-derived spheroids and organoids as a mode to screen for anticancer drugs.
Collapse
Affiliation(s)
| | - Elyn Amiela Salleh
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Marahaini Musa
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| |
Collapse
|
2
|
Sakahara M, Okamoto T, Srivastava U, Natsume Y, Yamanaka H, Suzuki Y, Obama K, Nagayama S, Yao R. Paneth-like cells produced from OLFM4 + stem cells support OLFM4 + stem cell growth in advanced colorectal cancer. Commun Biol 2024; 7:27. [PMID: 38182890 PMCID: PMC10770338 DOI: 10.1038/s42003-023-05504-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 10/25/2023] [Indexed: 01/07/2024] Open
Abstract
Tumor tissues consist of heterogeneous cells that originate from stem cells; however, their cell fate determination program remains incompletely understood. Using patient-derived organoids established from patients with advanced colorectal cancer (CRC), we evaluated the potential of olfactomedin 4 (OLFM4)+ stem cells to produce a bifurcated lineage of progenies with absorptive and secretory properties. In the early phases of organoid reconstruction, OLFM4+ cells preferentially gave rise to secretory cells. Additionally, we found that Paneth-like cells, which do not exist in the normal colon, were induced in response to Notch signaling inhibition. Video recordings of single OLFM4+ cells revealed that organoids containing Paneth-like cells were effectively propagated and that their selective ablation led to organoid collapse. In tumor tissues, Paneth-like cells were identified only in the region where tumor cells lost cell adhesion. These findings indicate that Paneth-like cells are directly produced by OLFM4+ stem cells and that their interaction contributes to tumor formation by providing niche factors. This study reveals the importance of the cell fate specification program for building a complete tumor cellular ecosystem, which might be targeted with novel therapeutics.
Collapse
Affiliation(s)
- Mizuho Sakahara
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takuya Okamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Upasna Srivastava
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Child Study Center, Yale School of Medicine, New Haven, CT, USA
| | - Yasuko Natsume
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kazutaka Obama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoshi Nagayama
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Surgery, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.
| |
Collapse
|
3
|
Chen S, Jiang W, Du Y, Yang M, Pan Y, Li H, Cui M. Single-cell analysis technologies for cancer research: from tumor-specific single cell discovery to cancer therapy. Front Genet 2023; 14:1276959. [PMID: 37900181 PMCID: PMC10602688 DOI: 10.3389/fgene.2023.1276959] [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: 08/13/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Single-cell sequencing (SCS) technology is changing our understanding of cellular components, functions, and interactions across organisms, because of its inherent advantage of avoiding noise resulting from genotypic and phenotypic heterogeneity across numerous samples. By directly and individually measuring multiple molecular characteristics of thousands to millions of single cells, SCS technology can characterize multiple cell types and uncover the mechanisms of gene regulatory networks, the dynamics of transcription, and the functional state of proteomic profiling. In this context, we conducted systematic research on SCS techniques, including the fundamental concepts, procedural steps, and applications of scDNA, scRNA, scATAC, scCITE, and scSNARE methods, focusing on the unique clinical advantages of SCS, particularly in cancer therapy. We have explored challenging but critical areas such as circulating tumor cells (CTCs), lineage tracing, tumor heterogeneity, drug resistance, and tumor immunotherapy. Despite challenges in managing and analyzing the large amounts of data that result from SCS, this technique is expected to reveal new horizons in cancer research. This review aims to emphasize the key role of SCS in cancer research and promote the application of single-cell technologies to cancer therapy.
Collapse
Affiliation(s)
- Siyuan Chen
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Weibo Jiang
- Department of Orthopaedic, The Second Hospital of Jilin University, Changchun, China
| | - Yanhui Du
- Department of Orthopaedics, Jilin Province People’s Hospital, Changchun, China
| | - Manshi Yang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yihan Pan
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Huan Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Mengying Cui
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| |
Collapse
|
4
|
Khatib TO, Amanso AM, Knippler CM, Pedro B, Summerbell ER, Zohbi NM, Konen JM, Mouw JK, Marcus AI. A live-cell platform to isolate phenotypically defined subpopulations for spatial multi-omic profiling. PLoS One 2023; 18:e0292554. [PMID: 37819930 PMCID: PMC10566726 DOI: 10.1371/journal.pone.0292554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 09/22/2023] [Indexed: 10/13/2023] Open
Abstract
Numerous techniques have been employed to deconstruct the heterogeneity observed in normal and diseased cellular populations, including single cell RNA sequencing, in situ hybridization, and flow cytometry. While these approaches have revolutionized our understanding of heterogeneity, in isolation they cannot correlate phenotypic information within a physiologically relevant live-cell state with molecular profiles. This inability to integrate a live-cell phenotype-such as invasiveness, cell:cell interactions, and changes in spatial positioning-with multi-omic data creates a gap in understanding cellular heterogeneity. We sought to address this gap by employing lab technologies to design a detailed protocol, termed Spatiotemporal Genomic and Cellular Analysis (SaGA), for the precise imaging-based selection, isolation, and expansion of phenotypically distinct live cells. This protocol requires cells expressing a photoconvertible fluorescent protein and employs live cell confocal microscopy to photoconvert a user-defined single cell or set of cells displaying a phenotype of interest. The total population is then extracted from its microenvironment, and the optically highlighted cells are isolated using fluorescence activated cell sorting. SaGA-isolated cells can then be subjected to multi-omics analysis or cellular propagation for in vitro or in vivo studies. This protocol can be applied to a variety of conditions, creating protocol flexibility for user-specific research interests. The SaGA technique can be accomplished in one workday by non-specialists and results in a phenotypically defined cellular subpopulations for integration with multi-omics techniques. We envision this approach providing multi-dimensional datasets exploring the relationship between live cell phenotypes and multi-omic heterogeneity within normal and diseased cellular populations.
Collapse
Affiliation(s)
- Tala O. Khatib
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute of Emory University, Atlanta, Georgia, United States of America
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia, United States of America
| | - Angelica M. Amanso
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute of Emory University, Atlanta, Georgia, United States of America
| | - Christina M. Knippler
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute of Emory University, Atlanta, Georgia, United States of America
| | - Brian Pedro
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Emily R. Summerbell
- Office of Intramural Training and Education, The National Institutes of Health, Bethesda, Maryland, United States of America
| | - Najdat M. Zohbi
- Graduate Medical Education, Piedmont Macon Medical, Macon, Georgia, United States of America
| | - Jessica M. Konen
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute of Emory University, Atlanta, Georgia, United States of America
| | - Janna K. Mouw
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute of Emory University, Atlanta, Georgia, United States of America
| | - Adam I. Marcus
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute of Emory University, Atlanta, Georgia, United States of America
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia, United States of America
| |
Collapse
|
5
|
Zheng Y, Wang X, Yang X, Xing N. Single-cell RNA sequencing reveals the cellular and molecular characteristics of high-grade and metastatic bladder cancer. Cell Oncol (Dordr) 2023; 46:1415-1427. [PMID: 37170046 DOI: 10.1007/s13402-023-00820-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
PURPOSE Metastatic bladder cancer (BC) has the highest somatic mutation frequency and recurrence rate of all tumors. However, the cellular and molecular characteristics of BC remain unclear. METHODS We performed single-cell RNA sequencing (scRNA-seq) on the samples of paracancerous normal tissue (PNT), primary tumor (PT) and lymph node metastasis (LNM). The proportions and gene expression profiles of different cell types in the tumor microenvironment (TME) were investigated. RESULTS In total, 50,158 cells were classified into six populations. Malignant cells of PT and LNM exhibited large mutant DNA fragments, while the cell phenotypes and gene expression profiles differed during differentiation. Metastasis was associated with a poorer prognosis than PT. Tumor-associated stromal cells and inhibitory immune cells were the main cell populations in PT and LNM. Cell-cell communication analysis revealed the roles of signaling pathways of inflammatory cancer-associated fibroblast (iCAF) and tumor-associated macrophage (TAM) in exhaustion of T cells. In addition, iCAF may recruit TAM to promote formation of the TME earlier than the differentiation of tumor cells. CONCLUSION This study through scRNA-seq enhanced our understanding of new features about the cellular and molecular similarities and differences of high-grade and metastatic bladder cancer, which might provide potential therapeutic targets in future treatment.
Collapse
Affiliation(s)
- Yue Zheng
- Department of Biochemistry and Molecular Biology, Basic Medical College, Shanxi Medical University, No. 56, Xinjiang South Road, Yingze street, Yingze District, Taiyuan City, 030000, Shanxi Province, China
| | - Xin Wang
- Department of Urology, First Hospital of Shanxi Medical University, No. 85, Jiefang South Road, Yingze street, Yingze District, Taiyuan City, 030000, Shanxi Province, China
| | - Xiaofeng Yang
- Department of Urology, First Hospital of Shanxi Medical University, No. 85, Jiefang South Road, Yingze street, Yingze District, Taiyuan City, 030000, Shanxi Province, China.
| | - Nianzeng Xing
- Department of Urology and State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing City, 100021, China
- Department of Urology, Shanxi Hospital Affiliated to Cancer Hospital, Cancer Hospital, Shanxi Province Cancer Hospital, Chinese Academy of Medical Sciences, Shanxi Medical University, Taiyuan, 030013, Shanxi Province, China
| |
Collapse
|
6
|
Yang C, Xiao W, Wang R, Hu Y, Yi K, Sun X, Wang G, Xu X. Tumor organoid model of colorectal cancer (Review). Oncol Lett 2023; 26:328. [PMID: 37415635 PMCID: PMC10320425 DOI: 10.3892/ol.2023.13914] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/01/2023] [Indexed: 07/08/2023] Open
Abstract
The establishment of self-organizing 'mini-gut' organoid models has brought about a significant breakthrough in biomedical research. Patient-derived tumor organoids have emerged as valuable tools for preclinical studies, offering the retention of genetic and phenotypic characteristics of the original tumor. These organoids have applications in various research areas, including in vitro modelling, drug discovery and personalized medicine. The present review provided an overview of intestinal organoids, focusing on their unique characteristics and current understanding. The progress made in colorectal cancer (CRC) organoid models was then delved into, discussing their role in drug development and personalized medicine. For instance, it has been indicated that patient-derived tumor organoids are able to predict response to irinotecan-based neoadjuvant chemoradiotherapy. Furthermore, the limitations and challenges associated with current CRC organoid models were addressed, along with proposed strategies for enhancing their utility in future basic and translational research.
Collapse
Affiliation(s)
- Chi Yang
- Department of Gastroenterology, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
| | - Wangwen Xiao
- Central Laboratory, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
| | - Rui Wang
- School of Pharmacy, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Yan Hu
- Central Laboratory, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
| | - Ke Yi
- Central Laboratory, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
| | - Xuan Sun
- Department of Gastroenterology, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
| | - Guanghui Wang
- School of Pharmacy, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Xiaohui Xu
- Department of Gastroenterology, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
- Central Laboratory, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
| |
Collapse
|
7
|
Schaaf CR, Polkoff KM, Carter A, Stewart AS, Sheahan B, Freund J, Ginzel J, Snyder JC, Roper J, Piedrahita JA, Gonzalez LM. A LGR5 reporter pig model closely resembles human intestine for improved study of stem cells in disease. FASEB J 2023; 37:e22975. [PMID: 37159340 PMCID: PMC10446885 DOI: 10.1096/fj.202300223r] [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: 02/07/2023] [Revised: 04/12/2023] [Accepted: 05/01/2023] [Indexed: 05/11/2023]
Abstract
Intestinal epithelial stem cells (ISCs) are responsible for intestinal epithelial barrier renewal; thereby, ISCs play a critical role in intestinal pathophysiology research. While transgenic ISC reporter mice are available, advanced translational studies lack a large animal model. This study validates ISC isolation in a new porcine Leucine Rich Repeat Containing G Protein-Coupled Receptor 5 (LGR5) reporter line and demonstrates the use of these pigs as a novel colorectal cancer (CRC) model. We applied histology, immunofluorescence, fluorescence-activated cell sorting, flow cytometry, gene expression quantification, and 3D organoid cultures to whole tissue and single cells from the duodenum, jejunum, ileum, and colon of LGR5-H2B-GFP and wild-type pigs. Ileum and colon LGR5-H2B-GFP, healthy human, and murine biopsies were compared by mRNA fluorescent in situ hybridization (FISH). To model CRC, adenomatous polyposis coli (APC) mutation was induced by CRISPR/Cas9 editing in porcine LGR5-H2B-GFP colonoids. Crypt-base, green fluorescent protein (GFP) expressing cells co-localized with ISC biomarkers. LGR5-H2B-GFPhi cells had significantly higher LGR5 expression (p < .01) and enteroid forming efficiency (p < .0001) compared with LGR5-H2B-GFPmed/lo/neg cells. Using FISH, similar LGR5, OLFM4, HOPX, LYZ, and SOX9 expression was identified between human and LGR5-H2B-GFP pig crypt-base cells. LGR5-H2B-GFP/APCnull colonoids had cystic growth in WNT/R-spondin-depleted media and significantly upregulated WNT/β-catenin target gene expression (p < .05). LGR5+ ISCs are reproducibly isolated in LGR5-H2B-GFP pigs and used to model CRC in an organoid platform. The known anatomical and physiologic similarities between pig and human, and those shown by crypt-base FISH, underscore the significance of this novel LGR5-H2B-GFP pig to translational ISC research.
Collapse
Affiliation(s)
- Cecilia R. Schaaf
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Kathryn M. Polkoff
- Department of Molecular Biomedical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Amber Carter
- Department of Molecular Biomedical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Amy S. Stewart
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Breanna Sheahan
- Department of Molecular Biomedical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - John Freund
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Joshua Ginzel
- Department of SurgeryDuke UniversityDurhamNorth CarolinaUSA
| | - Joshua C. Snyder
- Department of SurgeryDuke UniversityDurhamNorth CarolinaUSA
- Department of Cell BiologyDuke UniversityDurhamNorth CarolinaUSA
| | - Jatin Roper
- Department of Medicine, Division of GastroenterologyDuke UniversityDurhamNorth CarolinaUSA
- Department of Pharmacology and Cancer BiologyDuke UniversityDurhamNorth CarolinaUSA
| | - Jorge A. Piedrahita
- Department of Molecular Biomedical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Liara M. Gonzalez
- Department of Clinical Sciences, College of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| |
Collapse
|
8
|
Smirnov A, Melino G, Candi E. Gene expression in organoids: an expanding horizon. Biol Direct 2023; 18:11. [PMID: 36964575 PMCID: PMC10038780 DOI: 10.1186/s13062-023-00360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/20/2023] [Indexed: 03/26/2023] Open
Abstract
Recent development of human three-dimensional organoid cultures has opened new doors and opportunities ranging from modelling human development in vitro to personalised cancer therapies. These new in vitro systems are opening new horizons to the classic understanding of human development and disease. However, the complexity and heterogeneity of these models requires cutting-edge techniques to capture and trace global changes in gene expression to enable identification of key players and uncover the underlying molecular mechanisms. Rapid development of sequencing approaches made possible global transcriptome analyses and epigenetic profiling. Despite challenges in organoid culture and handling, these techniques are now being adapted to embrace organoids derived from a wide range of human tissues. Here, we review current state-of-the-art multi-omics technologies, such as single-cell transcriptomics and chromatin accessibility assays, employed to study organoids as a model for development and a platform for precision medicine.
Collapse
Affiliation(s)
- Artem Smirnov
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00166, Rome, Italy.
| |
Collapse
|
9
|
Song S, Feng L, Xi K, Sun Z, Kong D, Luo Z, Pei W, Zhang H. Single-cell profiling of the copy-number heterogeneity in colorectal cancer. Chin Med J (Engl) 2023; 136:707-718. [PMID: 36914941 PMCID: PMC10129169 DOI: 10.1097/cm9.0000000000002469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND With functionally heterogeneous cells, tumors comprise a complex ecosystem to promote tumor adaptability and evolution under strong selective pressure from the given microenvironment. Diversifying tumor cells or intra-tumor heterogeneity is essential for tumor growth, invasion, and immune evasion. However, no reliable method to classify tumor cell subtypes is yet available. In this study, we introduced the single-cell sequencing combined with copy number characteristics to identify the types of tumor cells in microsatellite stable (MSS) colorectal cancer (CRC). METHODS To characterize the somatic copy number alteration (SCNA) of MSS CRC in a single cell profile, we analyzed 26 tissue samples from 19 Korean patients (GSE132465, the Samsung Medical Center [SMC] dataset) and then verified our findings with 15 tissue samples from five Belgian patients (GSE144735, the Katholieke Universiteit Leuven 3 [KUL3] dataset). The Cancer Genome Atlas (TCGA) cohort, GSE39582 cohort, and National Cancer Center (NCC) cohort (24 MSS CRC patients were enrolled in this study between March 2017 and October 2017) were used to validate the clinical features of prognostic signatures. RESULTS We employed single cell RNA-sequencing data to identify three types of tumor cells in MSS CRC by their SCNA characteristics. Among these three types of tumor cells, C1 and C3 had a higher SCNA burden; C1 had significant chromosome 13 and 20 amplification, whereas C3 was the polar opposite of C1, which exhibited deletion in chromosome 13 and 20. The three types of tumor cells exhibited various functions in the tumor microenvironment and harbored different mutations. C1 and C2 were linked to the immune response and hypoxia, respectively, while C3 was critical for cell adhesion activity and tumor angiogenesis. Additionally, one gene ( OLFM4 ) was identified as epithelium-specific biomarker of better prognosis of CRC (TCGA cohort: P = 0.0110; GSE39582 cohort: P = 0.0098; NCC cohort: P = 0.0360). CONCLUSIONS On the basis of copy number characteristics, we illustrated tumor heterogeneity in MSS CRC and identified three types of tumor cells with distinct roles in tumor microenvironment. By understanding heterogeneity in the intricate tumor microenvironment, we gained an insight into the mechanisms of tumor evolution, which may support the development of therapeutic strategies.
Collapse
Affiliation(s)
- Shiyu Song
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Kexing Xi
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhigang Sun
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Deyang Kong
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhenkai Luo
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wei Pei
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Haizeng Zhang
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| |
Collapse
|
10
|
Khatib TO, Amanso AM, Pedro B, Knippler CM, Summerbell ER, Zohbi NM, Konen JM, Mouw JK, Marcus AI. A live-cell platform to isolate phenotypically defined subpopulations for spatial multi-omic profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530493. [PMID: 36909653 PMCID: PMC10002729 DOI: 10.1101/2023.02.28.530493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Numerous techniques have been employed to deconstruct the heterogeneity observed in normal and diseased cellular populations, including single cell RNA sequencing, in situ hybridization, and flow cytometry. While these approaches have revolutionized our understanding of heterogeneity, in isolation they cannot correlate phenotypic information within a physiologically relevant live-cell state, with molecular profiles. This inability to integrate a historical live-cell phenotype, such as invasiveness, cell:cell interactions, and changes in spatial positioning, with multi-omic data, creates a gap in understanding cellular heterogeneity. We sought to address this gap by employing lab technologies to design a detailed protocol, termed Spatiotemporal Genomics and Cellular Analysis (SaGA), for the precise imaging-based selection, isolation, and expansion of phenotypically distinct live-cells. We begin with cells stably expressing a photoconvertible fluorescent protein and employ live cell confocal microscopy to photoconvert a user-defined single cell or set of cells displaying a phenotype of interest. The total population is then extracted from its microenvironment, and the optically highlighted cells are isolated using fluorescence activated cell sorting. SaGA-isolated cells can then be subjected to multi-omics analysis or cellular propagation for in vitro or in vivo studies. This protocol can be applied to a variety of conditions, creating protocol flexibility for user-specific research interests. The SaGA technique can be accomplished in one workday by non-specialists and results in a phenotypically defined cellular subpopulation for integration with multi-omics techniques. We envision this approach providing multi-dimensional datasets exploring the relationship between live-cell phenotype and multi-omic heterogeneity within normal and diseased cellular populations.
Collapse
Affiliation(s)
- Tala O Khatib
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, USA
- Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia, USA
- These authors contributed equally
| | - Angelica M Amanso
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, USA
- Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
- These authors contributed equally
| | - Brian Pedro
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Christina M Knippler
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, USA
- Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Emily R Summerbell
- Office of Intratumoral Training and Education, The National Institutes of Health, Bethesda, Maryland, USA
| | - Najdat M Zohbi
- Graduate Medical Education, Piedmont Macon Medical, Macon, Georgia, USA
| | - Jessica M Konen
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, USA
- Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Janna K Mouw
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, USA
- Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Adam I Marcus
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, USA
- Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, Georgia, USA
| |
Collapse
|
11
|
Saeki S, Kumegawa K, Takahashi Y, Yang L, Osako T, Yasen M, Otsuji K, Miyata K, Yamakawa K, Suzuka J, Sakimoto Y, Ozaki Y, Takano T, Sano T, Noda T, Ohno S, Yao R, Ueno T, Maruyama R. Transcriptomic intratumor heterogeneity of breast cancer patient-derived organoids may reflect the unique biological features of the tumor of origin. Breast Cancer Res 2023; 25:21. [PMID: 36810117 PMCID: PMC9942352 DOI: 10.1186/s13058-023-01617-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/10/2023] [Indexed: 02/23/2023] Open
Abstract
BACKGROUND The intratumor heterogeneity (ITH) of cancer cells plays an important role in breast cancer resistance and recurrence. To develop better therapeutic strategies, it is necessary to understand the molecular mechanisms underlying ITH and their functional significance. Patient-derived organoids (PDOs) have recently been utilized in cancer research. They can also be used to study ITH as cancer cell diversity is thought to be maintained within the organoid line. However, no reports investigated intratumor transcriptomic heterogeneity in organoids derived from patients with breast cancer. This study aimed to investigate transcriptomic ITH in breast cancer PDOs. METHODS We established PDO lines from ten patients with breast cancer and performed single-cell transcriptomic analysis. First, we clustered cancer cells for each PDO using the Seurat package. Then, we defined and compared the cluster-specific gene signature (ClustGS) corresponding to each cell cluster in each PDO. RESULTS Cancer cells were clustered into 3-6 cell populations with distinct cellular states in each PDO line. We identified 38 clusters with ClustGS in 10 PDO lines and used Jaccard similarity index to compare the similarity of these signatures. We found that 29 signatures could be categorized into 7 shared meta-ClustGSs, such as those related to the cell cycle or epithelial-mesenchymal transition, and 9 signatures were unique to single PDO lines. These unique cell populations appeared to represent the characteristics of the original tumors derived from patients. CONCLUSIONS We confirmed the existence of transcriptomic ITH in breast cancer PDOs. Some cellular states were commonly observed in multiple PDOs, whereas others were specific to single PDO lines. The combination of these shared and unique cellular states formed the ITH of each PDO.
Collapse
Affiliation(s)
- Sumito Saeki
- grid.410807.a0000 0001 0037 4131Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550 Japan ,grid.410807.a0000 0001 0037 4131Breast Surgical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kohei Kumegawa
- grid.410807.a0000 0001 0037 4131Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yoko Takahashi
- grid.410807.a0000 0001 0037 4131Breast Surgical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Liying Yang
- grid.410807.a0000 0001 0037 4131Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550 Japan
| | - Tomo Osako
- grid.410807.a0000 0001 0037 4131Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mahmut Yasen
- grid.410807.a0000 0001 0037 4131Cancer Informatics and Biobanking Platform Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kazutaka Otsuji
- grid.410807.a0000 0001 0037 4131Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kenichi Miyata
- grid.410807.a0000 0001 0037 4131Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550 Japan
| | - Kaoru Yamakawa
- grid.410807.a0000 0001 0037 4131Cancer Informatics and Biobanking Platform Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Jun Suzuka
- grid.410807.a0000 0001 0037 4131Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuri Sakimoto
- grid.410807.a0000 0001 0037 4131Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550 Japan
| | - Yukinori Ozaki
- grid.410807.a0000 0001 0037 4131Breast Medical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Toshimi Takano
- grid.410807.a0000 0001 0037 4131Breast Medical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takeshi Sano
- grid.410807.a0000 0001 0037 4131Department of Gastroenterological Surgery, Gastroenterological Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tetsuo Noda
- grid.410807.a0000 0001 0037 4131Director’s Room, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Shinji Ohno
- grid.410807.a0000 0001 0037 4131Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryoji Yao
- grid.410807.a0000 0001 0037 4131Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takayuki Ueno
- grid.410807.a0000 0001 0037 4131Breast Surgical Oncology, Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550, Japan. .,Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan.
| |
Collapse
|
12
|
Jaitner S, Pretzsch E, Neumann J, Schäffauer A, Schiemann M, Angele M, Kumbrink J, Schwitalla S, Greten FR, Brandl L, Klauschen F, Horst D, Kirchner T, Jung A. Olfactomedin 4 associates with expression of differentiation markers but not with properties of cancer stemness, EMT nor metastatic spread in colorectal cancer. J Pathol Clin Res 2023; 9:73-85. [PMID: 36349502 PMCID: PMC9732686 DOI: 10.1002/cjp2.300] [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: 05/18/2022] [Revised: 10/06/2022] [Accepted: 10/13/2022] [Indexed: 11/11/2022]
Abstract
Tumor stem cells play a pivotal role in carcinogenesis and metastatic spread in colorectal cancer (CRC). Olfactomedin 4 (OLFM4) is co-expressed with the established stem cell marker leucine-rich repeat-containing G protein-coupled receptor 5 at the bottom of intestinal crypts and has been suggested as a surrogate for cancer stemness and a biomarker in gastrointestinal tumors associated with prognosis. Therefore, it was the aim of the present study to clarify whether OLFM4 is involved in carcinogenesis and metastatic spread in CRC. We used a combined approach of functional assays using forced OLFM4 overexpression in human CRC cell lines, xenograft mice, and an immunohistochemical approach using patient tissues to investigate the impact of OLFM4 on stemness, canonical Wnt signaling, properties of metastasis and differentiation as well as prognosis. OLFM4 expression correlated weakly with tumor grade in one patient cohort (metastasis collection: p = 0.05; pooled analysis of metastasis collection and survival collection: p = 0.19) and paralleled the expression of differentiation markers (FABP2, MUC2, and CK20) (p = 0.002) but did not correlate with stemness-associated markers. Further analyses in CRC cells lines as well as xenograft mice including forced overexpression of OLFM4 revealed that OLFM4 neither altered the expression of markers of stemness nor epithelial-mesenchymal transition, nor did OLFM4 itself drive proliferation, migration, or colony formation, which are all prerequisites of carcinogenesis and tumor progression. In line with this, we found no significant correlation between OLFM4 expression, metastasis, and patient survival. In summary, expression of OLFM4 in human CRC seems to be characteristic of differentiation marker expression in CRC but is not a driver of carcinogenesis nor metastatic spread.
Collapse
Affiliation(s)
- Stefanie Jaitner
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Elise Pretzsch
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany
| | - Jens Neumann
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany
| | - Achim Schäffauer
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Matthias Schiemann
- Institute of Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany.,Clinical Cooperation Group Immune Monitoring, Helmholtz Center Munich (Neuherberg) and Technische Universität München, Munich, Germany
| | - Martin Angele
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jörg Kumbrink
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany
| | - Sarah Schwitalla
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt, Germany
| | - Florian R Greten
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany.,Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt, Germany
| | - Lydia Brandl
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Frederick Klauschen
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany
| | - David Horst
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany
| | - Andreas Jung
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Munich, Heidelberg, Germany
| |
Collapse
|
13
|
Huang D, Li X, Liu Y, Yang J, Liu J, Zhang M, Liu X, Meng Q, Zhang S, Li H. Significance of differential expression of OLFM4 in the development of endometrial adenocarcinoma. Medicine (Baltimore) 2022; 101:e31858. [PMID: 36451436 PMCID: PMC9704920 DOI: 10.1097/md.0000000000031858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The incidence of endometrial adenocarcinoma (EA) has increased worldwide in recent years due to the widespread use of estrogen therapy and the overall increase in life expectancy. However, we know of no sensitive molecular index that can be used to predict the onset of EA, evaluate the therapeutic effects of treatment agents, or provide prognostic benefit in post-treatment follow-up. To explore the correlation between human olfactomedin 4 (OLFM4) and the clinicopathologic parameters of EA, and to determine the precise involvement of OLFM4 as a related factor in the occurrence and development of EA. We enrolled 61 gynecologic patients for a retrospective study at the Tai'an Central Hospital of Shandong Province from January 1, 2016, to June 30, 2022. We determined the expression levels of estrogen receptor α (ERα), progesterone receptor (PR), and OLFM4 proteins in endometrial tissue with the immunohistochemical S-P staining method, and analyzed the correlations among ERα, PR, and OLFM4 protein expression levels and with the pathologic stage, histologic grade, myometrial invasiveness, and lymphatic metastasis of EA. The expression levels of OLFM4 in EA were higher than in normal endometrium (P = .036). The expression level of OLFM4 protein in stage II-III patients was higher than that in stage I patients (P = .034), and the expression levels of ERα and PR proteins in EA were lower than those in normal endometrial tissue (P = .014 and P = .0005). While we observed no correlation in endometrial tissues of disparate pathologic types between OLFM4 and the expression levels of ERα and PR proteins, we noted a positive correlation between the expression levels of ERα and PR protein. The expression level of OLFM4 protein increased with the malignant degree of endometrial lesions and OLFM4 protein expression was related to the FIGO stage of EA. And OLFM4 protein can be used as 1 of the potential diagnostic factors for endometrial lesions, which is worthy of further study.
Collapse
Affiliation(s)
- Di Huang
- Shandong First Medical University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, China
| | - Xuefei Li
- Taian City Central Hospital of Qingdao University, Taian, China
| | - Yingzi Liu
- Taian City Central Hospital of Qingdao University, Taian, China
| | - Jie Yang
- Taian City Central Hospital of Qingdao University, Taian, China
| | - Jing Liu
- Taian City Central Hospital of Qingdao University, Taian, China
| | - Mingwei Zhang
- Taian City Central Hospital of Qingdao University, Taian, China
| | - Xiulan Liu
- Taian City Central Hospital of Qingdao University, Taian, China
| | - Qi Meng
- Taian City Central Hospital of Qingdao University, Taian, China
| | - Shuheng Zhang
- Taian City Central Hospital of Qingdao University, Taian, China
| | - Hua Li
- Taian City Central Hospital of Qingdao University, Taian, China
- * Correspondence: Hua Li, Taian City Central Hospital of Qingdao University, Taian 271000, China (e-mail: )
| |
Collapse
|
14
|
Zheng Y, Yang X. Application and prospect of single-cell sequencing in cancer metastasis. Future Oncol 2022; 18:2723-2736. [PMID: 35686493 DOI: 10.2217/fon-2022-0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cancer metastasis is a complicated process driven by internal genetic variations and developed through interactions with the external environment. This process usually causes therapeutic resistance and results in a low survival rate. In recent years, single-cell sequencing has become a popular method for revealing the tumor evolutionary genetic lineage, intra-tumoral heterogeneity and tumor microenvironment of the metastasis process. So as to find more therapeutic targets for clinical application, the spatial transcriptomics method has become a new rising field of cancer studies, which promotes the combination between clinical medicine and molecular biology. In future prospects, more accurate and personalized treatment models will come into reality.
Collapse
Affiliation(s)
- Yue Zheng
- Department of Biochemistry & Molecular Biology, Basic Medical College, Shanxi Medical University, Taiyuan City, Shanxi Province, 030000, China
| | - Xiaofeng Yang
- Department of Urology, First Hospital of Shanxi Medical University,Taiyuan City, Shanxi Province, 030000, China
| |
Collapse
|
15
|
Okamoto T, Natsume Y, Doi M, Nosato H, Iwaki T, Yamanaka H, Yamamoto M, Kawachi H, Noda T, Nagayama S, Sakanashi H, Yao R. Integration of human inspection and AI-based morphological typing of PDOs reveals inter-patient heterogeneity of colorectal cancer. Cancer Sci 2022; 113:2693-2703. [PMID: 35585758 PMCID: PMC9357621 DOI: 10.1111/cas.15396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/27/2022] [Accepted: 05/06/2022] [Indexed: 11/28/2022] Open
Abstract
Colorectal cancer (CRC) is a heterogenous disease, and patients have differences in therapeutic response. However, the mechanisms underlying inter-patient heterogeneity in the response to chemotherapeutic agents remain to be elucidated, and molecular tumor characteristics are required to select patients for specific therapies. Patient-derived organoids (PDOs) established from CRCs recapitulate various biological characteristics of tumor tissues, including cellular heterogeneity and the response to chemotherapy. PDOs established from CRCs exhibit various morphologies, but there are no criteria for defining these morphologies, which hampers the analysis of their biological significance. Here, we developed an artificial intelligence (AI)-based classifier to categorize PDOs based on microscopic images according to their similarity in appearance and classified tubular adenocarcinoma-derived PDOs into six types. Transcriptome analysis identified differential expression of genes related to cell adhesion in some of the morphological types. Genes involved in ribosome biogenesis were also differentially expressed and were most highly expressed in morphological types exhibiting CRC stem cell properties. We identified an RNA polymerase I inhibitor, CX-5641, to be an upstream regulator of these type-specific gene sets. Notably, PDO types with increased expression of genes involved in ribosome biogenesis were resistant to CX-5461 treatment. Taken together, these results uncover the biological significance of the morphology of PDOs and provide novel indicators by which to categorize CRCs. Therefore, the AI-based classifier is a useful tool to support PDO-based cancer research.
Collapse
Affiliation(s)
- Takuya Okamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuko Natsume
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Motomichi Doi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Hirokazu Nosato
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Toshiyuki Iwaki
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Mayuko Yamamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Hiroshi Kawachi
- Division of Pathology, Cancer Institute; Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tetsuo Noda
- Director's office, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Satoshi Nagayama
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Surgery, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Hidenori Sakanashi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| |
Collapse
|
16
|
Han Y, Wang D, Peng L, Huang T, He X, Wang J, Ou C. Single-cell sequencing: a promising approach for uncovering the mechanisms of tumor metastasis. J Hematol Oncol 2022; 15:59. [PMID: 35549970 PMCID: PMC9096771 DOI: 10.1186/s13045-022-01280-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/28/2022] [Indexed: 02/08/2023] Open
Abstract
Single-cell sequencing (SCS) is an emerging high-throughput technology that can be used to study the genomics, transcriptomics, and epigenetics at a single cell level. SCS is widely used in the diagnosis and treatment of various diseases, including cancer. Over the years, SCS has gradually become an effective clinical tool for the exploration of tumor metastasis mechanisms and the development of treatment strategies. Currently, SCS can be used not only to analyze metastasis-related malignant biological characteristics, such as tumor heterogeneity, drug resistance, and microenvironment, but also to construct metastasis-related cell maps for predicting and monitoring the dynamics of metastasis. SCS is also used to identify therapeutic targets related to metastasis as it provides insights into the distribution of tumor cell subsets and gene expression differences between primary and metastatic tumors. Additionally, SCS techniques in combination with artificial intelligence (AI) are used in liquid biopsy to identify circulating tumor cells (CTCs), thereby providing a novel strategy for treating tumor metastasis. In this review, we summarize the potential applications of SCS in the field of tumor metastasis and discuss the prospects and limitations of SCS to provide a theoretical basis for finding therapeutic targets and mechanisms of metastasis.
Collapse
Affiliation(s)
- Yingying Han
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Dan Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Lushan Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Tao Huang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Junpu Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,Department of Pathology, School of Basic Medicine, Central South University, Changsha, 410031, Hunan, China. .,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
| |
Collapse
|
17
|
Rees WD, Telkar N, Lin DTS, Wong MQ, Poloni C, Fathi A, Kobor M, Zachos NC, Steiner TS. An in vitro chronic damage model impairs inflammatory and regenerative responses in human colonoid monolayers. Cell Rep 2022; 38:110283. [PMID: 35045294 DOI: 10.1016/j.celrep.2021.110283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/20/2021] [Accepted: 12/28/2021] [Indexed: 12/18/2022] Open
Abstract
Acute damage to the intestinal epithelium can be repaired via de-differentiation of mature intestinal epithelial cells (IECs) to a stem-like state, but there is a lack of knowledge on how intestinal stem cells function after chronic injury, such as in inflammatory bowel disease (IBD). We developed a chronic-injury model in human colonoid monolayers by repeated rounds of air-liquid interface and submerged culture. We use this model to understand how chronic intestinal damage affects the ability of IECs to (1) respond to microbial stimulation, using the Toll-like receptor 5 (TLR5) agonist FliC and (2) regenerate and protect the epithelium from further damage. Repeated rounds of damage impair the ability of IECs to regrow and respond to TLR stimulation. We also identify mRNA expression and DNA methylation changes in genes associated with IBD and colon cancer. This methodology results in a human model of recurrent IEC injury like that which occurs in IBD.
Collapse
Affiliation(s)
- William D Rees
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada; Division of Hematology, Department of Medicine, Stanford University, Palo Alto, CA, USA
| | - Nikita Telkar
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada; BC Cancer Agency, University of British Columbia, Vancouver, BC, Canada
| | - David T S Lin
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - May Q Wong
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - Chad Poloni
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - Ayda Fathi
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - Michael Kobor
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - Nicholas C Zachos
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Theodore S Steiner
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada.
| |
Collapse
|
18
|
Wang J, Feng X, Li Z, Chen Y, Huang W. Patient-derived organoids as a model for tumor research. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 189:259-326. [PMID: 35595351 DOI: 10.1016/bs.pmbts.2022.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cancer represents a leading cause of death, despite the rapid progress of cancer research, leading to urgent need for accurate preclinical model to further study of tumor mechanism and accelerate translational applications. Cancer cell lines cannot fully recapitulate tumors of different patients due to the lack of tumor complexity and specification, while the high technical difficulty, long time, and substantial cost of patient-derived xenograft model makes it unable to be used extensively for all types of tumors and large-scale drug screening. Patient-derived organoids can be established rapidly with a high success rate from many tumors, and precisely replicate the key histopathological, genetic, and phenotypic features, as well as therapeutic response of patient tumor. Therefore, they are extensively used in cancer basic research, biobanking, disease modeling and precision medicine. The combinations of cancer organoids with other advanced technologies, such as 3D bio-printing, organ-on-a-chip, and CRISPR-Cas9, contributes to the more complete replication of complex tumor microenvironment and tumorigenesis. In this review, we discuss the various methods of the establishment and the application of patient-derived organoids in diverse tumors as well as the limitations and future prospects of these models. Further advances of tumor organoids are expected to bridge the huge gap between bench and bedside and provide the unprecedented opportunities to advance cancer research.
Collapse
Affiliation(s)
- Jia Wang
- The First Affiliated Hospital of Shantou University, Shantou University Medical College, Shantou, China
| | - Xiaoying Feng
- The First Affiliated Hospital of Shantou University, Shantou University Medical College, Shantou, China
| | - Zhichao Li
- Department of Urology, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China; Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, China; International Cancer Center of Shenzhen University, Shenzhen, China
| | - Yongsong Chen
- The First Affiliated Hospital of Shantou University, Shantou University Medical College, Shantou, China
| | - Weiren Huang
- The First Affiliated Hospital of Shantou University, Shantou University Medical College, Shantou, China; Department of Urology, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China; Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, China; International Cancer Center of Shenzhen University, Shenzhen, China; Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| |
Collapse
|
19
|
Okamoto T, Natsume Y, Yamanaka H, Fukuda M, Yao R. A protocol for efficient CRISPR-Cas9-mediated knock-in in colorectal cancer patient-derived organoids. STAR Protoc 2021; 2:100780. [PMID: 34585151 PMCID: PMC8455475 DOI: 10.1016/j.xpro.2021.100780] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Patient-derived organoids (PDOs) recapitulate the cellular heterogeneity of the original colorectal tumor tissue. Here, we describe a protocol to generate genetically modified PDOs to investigate cancer stem cells. This protocol uses the CRISPR-Cas9 system to knock-in the IRES-EGFP-P2A-iCaspase9 cassette into the 3′ UTR of the potential cancer stem cell marker gene, which allows us to investigate their potential for self-replication and pluripotency. We describe the procedure for generating mutant PDOs and their application for stem cell research. For complete details on the generation and use of this protocol, please refer to Okamoto et al. Okamoto et al. (2021). A detailed protocol for efficient CRISPR-Cas9 mediated knock-in in PDOs Generation of IRES-EGFP-P2A-iCaspase9 cassette for simple preparation of donor vector Visualization of cancer stem cells in PDOs using time-lapse imaging microscopy Specific elimination of cancer stem cells by adding AP20187
Collapse
Affiliation(s)
- Takuya Okamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan.,Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yasuko Natsume
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Mayuko Fukuda
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| |
Collapse
|
20
|
Organoids and Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13112657. [PMID: 34071313 PMCID: PMC8197877 DOI: 10.3390/cancers13112657] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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.
Collapse
|