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Yijiao C, Junhui A, Rong H, Yuliang L, Donghui W, Songrui L, Tongying F. Single-cell mRNA sequencing of giant panda (Ailuropoda melanoleuca) seminoma reveals the cellular and molecular characteristics of tumour cells. Vet Med Sci 2024; 10:e1348. [PMID: 38227708 PMCID: PMC10790506 DOI: 10.1002/vms3.1348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 01/18/2024] Open
Abstract
Testicular tumours are zoonoses that can occur in not only human, but other animals, include giant pandas. A middle-aged male giant panda named Fufu was diagnosed with a testicular tumour and underwent surgery to remove the entire left testis. The testis was mainly composed of three substantive parts: normal tissue on the outside, tumour tissue in the middle, and necrosis in the centre. HE stains revealed that the tumour was a seminoma. Single-cell mRNA sequence was applied to characterise cellular states and molecular circuitries of giant panda testicular seminoma. Only germ cell markers expressed in nearly all tumour cells, and the tumour cells appeared to be the same subtype of seminoma cells. We identified four clusters with unique genes expression. They were early apoptosis cells (EAC), inactive cells (IC), active cells subcluster 1 (AC-1) and active cells subcluster 2 (AC-2). We utilised monocle tools and found that IC cells was in the initiation stage, and EAC was one type of terminal stage, suggesting that tumour cells may undergo apoptosis in the future. AC-2 was another type of terminal stage, representing a group of progressive cells. Our study represents the first report to utilise scRNA-seq to characterise the cellular states and molecular circuitries of a giant panda testicular tumour. This investigation proposes CD117 and CD30 as dependable markers for future pathologic diagnosis. Our findings also suggest that CTSV and other genes with unique expression patterns in active and progressive giant panda seminoma cells may act as early prognostic biomarkers.
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Affiliation(s)
- Chen Yijiao
- Chengdu Research Base of Giant Panda BreedingChengduChina
- Sichuan Key Laboratory of Conservation Biology for Endangered WildlifeChengduChina
| | - An Junhui
- Chengdu Research Base of Giant Panda BreedingChengduChina
- Sichuan Key Laboratory of Conservation Biology for Endangered WildlifeChengduChina
- Sichuan Academy of Giant Panda ChengduChengduChina
| | - Hou Rong
- Chengdu Research Base of Giant Panda BreedingChengduChina
- Sichuan Key Laboratory of Conservation Biology for Endangered WildlifeChengduChina
- Sichuan Academy of Giant Panda ChengduChengduChina
| | - Liu Yuliang
- Chengdu Research Base of Giant Panda BreedingChengduChina
- Sichuan Key Laboratory of Conservation Biology for Endangered WildlifeChengduChina
- Sichuan Academy of Giant Panda ChengduChengduChina
| | - Wang Donghui
- Chengdu Research Base of Giant Panda BreedingChengduChina
- Sichuan Key Laboratory of Conservation Biology for Endangered WildlifeChengduChina
- Sichuan Academy of Giant Panda ChengduChengduChina
| | - Liu Songrui
- Chengdu Research Base of Giant Panda BreedingChengduChina
- Sichuan Key Laboratory of Conservation Biology for Endangered WildlifeChengduChina
- Sichuan Academy of Giant Panda ChengduChengduChina
| | - Feng Tongying
- Sichuan Key Laboratory of Conservation Biology for Endangered WildlifeChengduChina
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2
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Vanova T, Sedmik J, Raska J, Amruz Cerna K, Taus P, Pospisilova V, Nezvedova M, Fedorova V, Kadakova S, Klimova H, Capandova M, Orviska P, Fojtik P, Bartova S, Plevova K, Spacil Z, Hribkova H, Bohaciakova D. Cerebral organoids derived from patients with Alzheimer's disease with PSEN1/2 mutations have defective tissue patterning and altered development. Cell Rep 2023; 42:113310. [PMID: 37864790 DOI: 10.1016/j.celrep.2023.113310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/09/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023] Open
Abstract
During the past two decades, induced pluripotent stem cells (iPSCs) have been widely used to study human neural development and disease. Especially in the field of Alzheimer's disease (AD), remarkable effort has been put into investigating molecular mechanisms behind this disease. Then, with the advent of 3D neuronal cultures and cerebral organoids (COs), several studies have demonstrated that this model can adequately mimic familial and sporadic AD. Therefore, we created an AD-CO model using iPSCs derived from patients with familial AD forms and explored early events and the progression of AD pathogenesis. Our study demonstrated that COs derived from three AD-iPSC lines with PSEN1(A246E) or PSEN2(N141I) mutations developed the AD-specific markers in vitro, yet they also uncover tissue patterning defects and altered development. These findings are complemented by single-cell sequencing data confirming this observation and uncovering that neurons in AD-COs likely differentiate prematurely.
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Affiliation(s)
- Tereza Vanova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center (ICRC), St. Anne's University Hospital, 60200 Brno, Czech Republic
| | - Jiri Sedmik
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Jan Raska
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center (ICRC), St. Anne's University Hospital, 60200 Brno, Czech Republic
| | - Katerina Amruz Cerna
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Petr Taus
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Veronika Pospisilova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Marketa Nezvedova
- RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Veronika Fedorova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Sona Kadakova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Hana Klimova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Michaela Capandova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Petra Orviska
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Petr Fojtik
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center (ICRC), St. Anne's University Hospital, 60200 Brno, Czech Republic
| | - Simona Bartova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic; Institute of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, 61300 Brno, Czech Republic
| | - Zdenek Spacil
- RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Hana Hribkova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Dasa Bohaciakova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center (ICRC), St. Anne's University Hospital, 60200 Brno, Czech Republic.
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Rosowski S, Remmert C, Marder M, Akishiba M, Bushe J, Feuchtinger A, Platen A, Ussar S, Theis F, Wiedenmann S, Meier M. Single-cell characterization of neovascularization using hiPSC-derived endothelial cells in a 3D microenvironment. Stem Cell Reports 2023; 18:1972-1986. [PMID: 37714147 PMCID: PMC10656300 DOI: 10.1016/j.stemcr.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/17/2023] Open
Abstract
The formation of vascular structures is fundamental for in vitro tissue engineering. Vascularization can enable the nutrient supply within larger structures and increase transplantation efficiency. We differentiated human induced pluripotent stem cells toward endothelial cells in 3D suspension culture. To investigate in vitro neovascularization and various 3D microenvironmental approaches, we designed a comprehensive single-cell transcriptomic study. Time-resolved single-cell transcriptomics of the endothelial and co-evolving mural cells gave insights into cell type development, stability, and plasticity. Transfer to a 3D hydrogel microenvironment induced neovascularization and facilitated tracing of migrating, coalescing, and tubulogenic endothelial cell states. During maturation, we monitored two pericyte subtypes evolving mural cells. Profiling cell-cell interactions between pericytes and endothelial cells revealed angiogenic signals during tubulogenesis. In silico discovered ligands were tested for their capability to attract endothelial cells. Our data, analyses, and results provide an in vitro roadmap to guide vascularization in future tissue engineering.
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Affiliation(s)
- Simon Rosowski
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Caroline Remmert
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Maren Marder
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Misao Akishiba
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Judith Bushe
- Research Unit Analytical Pathology, Helmholtz München, 85764 Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz München, 85764 Neuherberg, Germany
| | - Alina Platen
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Siegfried Ussar
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany; Department of Mathematics, Technical University of Munich, 85748 Garching bei München, Germany
| | - Sandra Wiedenmann
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Matthias Meier
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany; University Leipzig, Center for Biotechnology and Biomedicine, Institute of Biochemistry, Leipzig, Germany.
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Jiang M, Yu H, Luo L, Zhang L, Xiong A, Wang J, Wang Q, Liu Y, Liu S, Xiong Y, Yang P, Chang C, Zhang J, He X, Li G. Single cell characteristics of patients with vaccine-related adverse reactions following inactivated COVID-19 vaccination. Hum Vaccin Immunother 2023; 19:2246542. [PMID: 37614152 PMCID: PMC10453975 DOI: 10.1080/21645515.2023.2246542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/26/2023] [Accepted: 08/06/2023] [Indexed: 08/25/2023] Open
Abstract
A good safety and immunogenicity profile was reported in Phase I and II clinical trials of inactivated SARS-CoV-2 vaccines. Here, we report two cases associated with vaccine-associated adverse events, including one patient with fever and another with anaphylactic shock resulting from inactivated SARS-CoV-2 vaccination. Cell sub-types and the importance of genetic characteristics were assessed using single-cell mRNA sequencing and machine learning. Overall, the patient with fever showed a significant increase in the numbers of cytotoxic CD8 T cells and MKI67high CD8 T cells. A potential concurrent infection with the Epstein-Barr virus enhanced interferon type I responses to vaccination against the virus. STAT1, E2F1, YBX1, and E2F7 played a key role in the transcription regulation of MKI67high CD8 T cells. In contrast, the patient with allergic shock displayed predominant increases in the numbers of S100A9high monocytes, activated CD4 T cells, and PPBPhigh megakaryocytes. The decision tree showed that LYZ and S100A8 in S100A9high monocytes contributed to the degranulation of neutrophils and activation of neutrophils involved in allergic shock. PPBP and PF4 were major contributors to platelet degranulation. These findings highlight the diversity of adverse reactions following inactivated SARS-CoV-2 vaccination and show the emerging role of cellular subtypes and central genes in vaccine-associated adverse reactions.
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Affiliation(s)
- Manling Jiang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Haiqiong Yu
- Department of Pulmonary and Critical Care Medicine, The Eight Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Li Luo
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Lei Zhang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Anying Xiong
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Junyi Wang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Qianhui Wang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Yao Liu
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Shengbin Liu
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Ying Xiong
- Department of Pulmonary and Critical Care Medicine, Sichuan friendship hospital, Chengdu, China
| | - Pingchang Yang
- Institute of Allergy & Immunology, Shenzhen University School of Medicine, State Key Laboratory of Respiratory Disease Allergy Division at Shenzhen University, Shenzhen, China
| | - Christopher Chang
- Division of Immunology, Allergy and Rheumatology, Joe DiMaggio Children’s Hospital, Memorial Healthcare System, Hollywood, FL, USA
| | - Jianquan Zhang
- Department of Pulmonary and Critical Care Medicine, The Eight Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Xiang He
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
| | - Guoping Li
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Pulmonary and Critical Care Medicine, Chengdu Third People’s Hospital Branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu, China
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5
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Jiang Y, He Y, Pan X, Wang P, Yuan X, Ma B. Advances in Oocyte Maturation In Vivo and In Vitro in Mammals. Int J Mol Sci 2023; 24:9059. [PMID: 37240406 PMCID: PMC10219173 DOI: 10.3390/ijms24109059] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The quality and maturation of an oocyte not only play decisive roles in fertilization and embryo success, but also have long-term impacts on the later growth and development of the fetus. Female fertility declines with age, reflecting a decline in oocyte quantity. However, the meiosis of oocytes involves a complex and orderly regulatory process whose mechanisms have not yet been fully elucidated. This review therefore mainly focuses on the regulation mechanism of oocyte maturation, including folliculogenesis, oogenesis, and the interactions between granulosa cells and oocytes, plus in vitro technology and nuclear/cytoplasm maturation in oocytes. Additionally, we have reviewed advances made in the single-cell mRNA sequencing technology related to oocyte maturation in order to improve our understanding of the mechanism of oocyte maturation and to provide a theoretical basis for subsequent research into oocyte maturation.
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Affiliation(s)
- Yao Jiang
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA 6149, Australia
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yingting He
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiangchun Pan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Penghao Wang
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA 6149, Australia
| | - Xiaolong Yuan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Bin Ma
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA 6149, Australia
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Alcaraz LB, Mallavialle A, Mollevi C, Boissière-Michot F, Mansouri H, Simony-Lafontaine J, Laurent-Matha V, Chardès T, Jacot W, Turtoi A, Roger P, Guiu S, Liaudet-Coopman E. SPARC in cancer-associated fibroblasts is an independent poor prognostic factor in non-metastatic triple-negative breast cancer and exhibits pro-tumor activity. Int J Cancer 2023; 152:1243-1258. [PMID: 36346290 PMCID: PMC10099777 DOI: 10.1002/ijc.34345] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype and lacks specific targeted therapeutic agents. The current mechanistic evidence from cell-based studies suggests that the matricellular protein SPARC has a tumor-promoting role in TNBC; however, data on the clinical relevance of SPARC expression/secretion by tumor and stromal cells in TNBC are limited. Here, we analyzed by immunohistochemistry the prognostic value of tumor and stromal cell SPARC expression in 148 patients with non-metastatic TNBC and long follow-up (median: 5.4 years). We also quantified PD-L1 and PD-1 expression. We detected SPARC expression in tumor cells (42.4%), cancer-associated fibroblasts (CAFs; 88.1%), tumor-associated macrophages (77.1%), endothelial cells (75.2%) and tumor-infiltrating lymphocytes (9.8%). Recurrence-free survival was significantly lower in patients with SPARC-expressing CAFs. Multivariate analysis showed that SPARC expression in CAFs was an independent prognostic factor. We also detected tumor and stromal cell SPARC expression in TNBC cytosols, and in patient-derived xenografts and cell lines. Furthermore, we analyzed publicly available single-cell mRNA sequencing data and found that in TNBC, SPARC is expressed by different CAF subpopulations, including myofibroblasts and inflammatory fibroblasts that are involved in tumor-related processes. We then showed that fibroblast-secreted SPARC had a tumor-promoting role by inhibiting TNBC cell adhesion and stimulating their motility and invasiveness. Overall, our study demonstrates that SPARC expression in CAFs is an independent prognostic marker of poor outcome in TNBC. Patients with SPARC-expressing CAFs could be eligible for anti-SPARC targeted therapy.
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Affiliation(s)
| | | | - Caroline Mollevi
- Biometry Unit, ICM, University of Montpellier, Montpellier, France.,Desbrest Institute of Epidemiology and Public Health, University of Montpellier, INSERM, Montpellier, France
| | | | - Hanane Mansouri
- IRCM, INSERM U1194, Univ Montpellier, ICM, Montpellier, France.,RHEM, IRCM, Montpellier, France
| | | | | | - Thierry Chardès
- IRCM, INSERM U1194, Univ Montpellier, ICM, Montpellier, France
| | - William Jacot
- IRCM, INSERM U1194, Univ Montpellier, ICM, Montpellier, France.,Translational Research Unit, ICM, Montpellier, France.,Department of Medical Oncology, ICM, Montpellier, France
| | - Andrei Turtoi
- IRCM, INSERM U1194, Univ Montpellier, ICM, Montpellier, France
| | - Pascal Roger
- IRCM, INSERM U1194, Univ Montpellier, ICM, Montpellier, France.,Department of Pathology, CHU, Nîmes, France
| | - Séverine Guiu
- IRCM, INSERM U1194, Univ Montpellier, ICM, Montpellier, France.,Department of Medical Oncology, ICM, Montpellier, France
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Corkins ME, Achieng M, DeLay BD, Krneta-Stankic V, Cain MP, Walker BL, Chen J, Lindström NO, Miller RK. A comparative study of cellular diversity between the Xenopus pronephric and mouse metanephric nephron. Kidney Int 2023; 103:77-86. [PMID: 36055600 PMCID: PMC9822858 DOI: 10.1016/j.kint.2022.07.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 01/11/2023]
Abstract
The kidney is an essential organ that ensures bodily fluid homeostasis and removes soluble waste products from the organism. Nephrons, the functional units of the kidney, comprise a blood filter, the glomerulus or glomus, and an epithelial tubule that processes the filtrate from the blood or coelom and selectively reabsorbs solutes, such as sugars, proteins, ions, and water, leaving waste products to be eliminated in the urine. Genes coding for transporters are segmentally expressed, enabling the nephron to sequentially process the filtrate. The Xenopus embryonic kidney, the pronephros, which consists of a single large nephron, has served as a valuable model to identify genes involved in nephron formation and patterning. Therefore, the developmental patterning program that generates these segments is of great interest. Prior work has defined the gene expression profiles of Xenopus nephron segments via in situ hybridization strategies, but a comprehensive understanding of the cellular makeup of the pronephric kidney remains incomplete. Here, we carried out single-cell mRNA sequencing of the functional Xenopus pronephric nephron and evaluated its cellular composition through comparative analyses with previous Xenopus studies and single-cell mRNA sequencing of the adult mouse kidney. This study reconstructs the cellular makeup of the pronephric kidney and identifies conserved cells, segments, and associated gene expression profiles. Thus, our data highlight significant conservation in podocytes, proximal and distal tubule cells, and divergence in cellular composition underlying the capacity of each nephron to remove wastes in the form of urine, while emphasizing the Xenopus pronephros as a model for physiology and disease.
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Affiliation(s)
- Mark E Corkins
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School, UTHealth Houston, Houston, Texas, USA.
| | - MaryAnne Achieng
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Bridget D DeLay
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School, UTHealth Houston, Houston, Texas, USA
| | - Vanja Krneta-Stankic
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School, UTHealth Houston, Houston, Texas, USA; Program in Genes and Development, MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Margo P Cain
- Department of Pulmonary Medicine, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Brandy L Walker
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School, UTHealth Houston, Houston, Texas, USA; Program in Genetics and Epigenetics, MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Jichao Chen
- Department of Pulmonary Medicine, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Program in Genetics and Epigenetics, MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Rachel K Miller
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School, UTHealth Houston, Houston, Texas, USA; Program in Genetics and Epigenetics, MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas, USA; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Program in Biochemistry and Cell Biology, MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas, USA.
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8
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Graeff M, Rana S, Wendrich JR, Dorier J, Eekhout T, Aliaga Fandino AC, Guex N, Bassel GW, De Rybel B, Hardtke CS. A single-cell morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root. Mol Plant 2021; 14:1985-1999. [PMID: 34358681 PMCID: PMC8674818 DOI: 10.1016/j.molp.2021.07.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/03/2021] [Accepted: 07/29/2021] [Indexed: 05/05/2023]
Abstract
The effects of brassinosteroid signaling on shoot and root development have been characterized in great detail but a simple consistent positive or negative impact on a basic cellular parameter was not identified. In this study, we combined digital 3D single-cell shape analysis and single-cell mRNA sequencing to characterize root meristems and mature root segments of brassinosteroid-blind mutants and wild type. The resultant datasets demonstrate that brassinosteroid signaling affects neither cell volume nor cell proliferation capacity. Instead, brassinosteroid signaling is essential for the precise orientation of cell division planes and the extent and timing of anisotropic cell expansion. Moreover, we found that the cell-aligning effects of brassinosteroid signaling can propagate to normalize the anatomy of both adjacent and distant brassinosteroid-blind cells through non-cell-autonomous functions, which are sufficient to restore growth vigor. Finally, single-cell transcriptome data discern directly brassinosteroid-responsive genes from genes that can react non-cell-autonomously and highlight arabinogalactans as sentinels of brassinosteroid-dependent anisotropic cell expansion.
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Affiliation(s)
- Moritz Graeff
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Surbhi Rana
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Jos R Wendrich
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9000 Ghent, Belgium
| | - Julien Dorier
- Bioinformatics Competence Center, University of Lausanne, Genopode Building, 1015 Lausanne, Switzerland
| | - Thomas Eekhout
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9000 Ghent, Belgium
| | - Ana Cecilia Aliaga Fandino
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Genopode Building, 1015 Lausanne, Switzerland
| | - George W Bassel
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9000 Ghent, Belgium
| | - Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland.
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9
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Kim HK, Ha TW, Lee MR. Single-Cell Transcriptome Analysis as a Promising Tool to Study Pluripotent Stem Cell Reprogramming. Int J Mol Sci 2021; 22:ijms22115988. [PMID: 34206025 PMCID: PMC8198005 DOI: 10.3390/ijms22115988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/15/2022] Open
Abstract
Cells are the basic units of all organisms and are involved in all vital activities, such as proliferation, differentiation, senescence, and apoptosis. A human body consists of more than 30 trillion cells generated through repeated division and differentiation from a single-cell fertilized egg in a highly organized programmatic fashion. Since the recent formation of the Human Cell Atlas consortium, establishing the Human Cell Atlas at the single-cell level has been an ongoing activity with the goal of understanding the mechanisms underlying diseases and vital cellular activities at the level of the single cell. In particular, transcriptome analysis of embryonic stem cells at the single-cell level is of great importance, as these cells are responsible for determining cell fate. Here, we review single-cell analysis techniques that have been actively used in recent years, introduce the single-cell analysis studies currently in progress in pluripotent stem cells and reprogramming, and forecast future studies.
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10
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Keuls RA, Parchem RJ. Single-Cell Multiomic Approaches Reveal Diverse Labeling of the Nervous System by Common Cre-Drivers. Front Cell Neurosci 2021; 15:648570. [PMID: 33935652 PMCID: PMC8079645 DOI: 10.3389/fncel.2021.648570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/15/2021] [Indexed: 11/27/2022] Open
Abstract
Neural crest development involves a series of dynamic, carefully coordinated events that result in human disease when not properly orchestrated. Cranial neural crest cells acquire unique multipotent developmental potential upon specification to generate a broad variety of cell types. Studies of early mammalian neural crest and nervous system development often use the Cre-loxP system to lineage trace and mark cells for further investigation. Here, we carefully profile the activity of two common neural crest Cre-drivers at the end of neurulation in mice. RNA sequencing of labeled cells at E9.5 reveals that Wnt1-Cre2 marks cells with neuronal characteristics consistent with neuroepithelial expression, whereas Sox10-Cre predominantly labels the migratory neural crest. We used single-cell mRNA and single-cell ATAC sequencing to profile the expression of Wnt1 and Sox10 and identify transcription factors that may regulate the expression of Wnt1-Cre2 in the neuroepithelium and Sox10-Cre in the migratory neural crest. Our data identify cellular heterogeneity during cranial neural crest development and identify specific populations labeled by two Cre-drivers in the developing nervous system.
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Affiliation(s)
- Rachel A. Keuls
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, United States
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Ronald J. Parchem
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, United States
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
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11
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Walsh SM, Sheridan RM, Lucas ED, Doan TA, Ware BC, Schafer J, Fu R, Burchill MA, Hesselberth JR, Tamburini BAJ. Molecular tracking devices quantify antigen distribution and archiving in the murine lymph node. eLife 2021; 10:e62781. [PMID: 33843587 PMCID: PMC8116055 DOI: 10.7554/elife.62781] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/09/2021] [Indexed: 01/02/2023] Open
Abstract
The detection of foreign antigens in vivo has relied on fluorescent conjugation or indirect read-outs such as antigen presentation. In our studies, we found that these widely used techniques had several technical limitations that have precluded a complete picture of antigen trafficking or retention across lymph node cell types. To address these limitations, we developed a 'molecular tracking device' to follow the distribution, acquisition, and retention of antigen in the lymph node. Utilizing an antigen conjugated to a nuclease-resistant DNA tag, acting as a combined antigen-adjuvant conjugate, and single-cell mRNA sequencing, we quantified antigen abundance in the lymph node. Variable antigen levels enabled the identification of caveolar endocytosis as a mechanism of antigen acquisition or retention in lymphatic endothelial cells. Thus, these molecular tracking devices enable new approaches to study dynamic tissue dissemination of antigen-adjuvant conjugates and identify new mechanisms of antigen acquisition and retention at cellular resolution in vivo.
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Affiliation(s)
- Shannon M Walsh
- Department of Biochemistry and Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Ryan M Sheridan
- RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
| | - Erin D Lucas
- Immunology Graduate Program, University of Colorado School of MedicineAuroraUnited States
- Department of Immunology and Microbiology, University of Colorado School of MedicineAuroraUnited States
| | - Thu A Doan
- Immunology Graduate Program, University of Colorado School of MedicineAuroraUnited States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Colorado School of MedicineAuroraUnited States
| | - Brian C Ware
- Immunology Graduate Program, University of Colorado School of MedicineAuroraUnited States
- Department of Immunology and Microbiology, University of Colorado School of MedicineAuroraUnited States
| | - Johnathon Schafer
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Colorado School of MedicineAuroraUnited States
| | - Rui Fu
- RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
| | - Matthew A Burchill
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Colorado School of MedicineAuroraUnited States
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
- RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
| | - Beth Ann Jiron Tamburini
- Immunology Graduate Program, University of Colorado School of MedicineAuroraUnited States
- Department of Immunology and Microbiology, University of Colorado School of MedicineAuroraUnited States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Colorado School of MedicineAuroraUnited States
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12
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Lan T, Hutvagner G, Lan Q, Liu T, Li J. Sequencing dropout-and-batch effect normalization for single-cell mRNA profiles: a survey and comparative analysis. Brief Bioinform 2020; 22:5929825. [PMID: 33073843 DOI: 10.1093/bib/bbaa248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/30/2020] [Accepted: 09/03/2020] [Indexed: 12/22/2022] Open
Abstract
Single-cell mRNA sequencing has been adopted as a powerful technique for understanding gene expression profiles at the single-cell level. However, challenges remain due to factors such as the inefficiency of mRNA molecular capture, technical noises and separate sequencing of cells in different batches. Normalization methods have been developed to ensure a relatively accurate analysis. This work presents a survey on 10 tools specifically designed for single-cell mRNA sequencing data preprocessing steps, among which 6 tools are used for dropout normalization and 4 tools are for batch effect correction. In this survey, we outline the main methodology for each of these tools, and we also compare these tools to evaluate their normalization performance on datasets which are simulated under the constraints of dropout inefficiency, batch effect or their combined effects. We found that Saver and Baynorm performed better than other methods in dropout normalization, in most cases. Beer and Batchelor performed better in the batch effect normalization, and the Saver-Beer tool combination and the Baynorm-Beer combination performed better in the mixed dropout-and-batch effect normalization. Over-normalization is a common issue occurred to these dropout normalization tools that is worth of future investigation. For the batch normalization tools, the capability of retaining heterogeneity between different groups of cells after normalization can be another direction for future improvement.
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Affiliation(s)
- Tian Lan
- Faculty of Engineering and IT in the University of Technology Sydney
| | - Gyorgy Hutvagner
- School of Biomedical Engineering, University of Technology Sydney
| | - Qing Lan
- Neurosurgical Department of Second Affiliated Hospital of Soochow University
| | - Tao Liu
- Children's Cancer Institute Australia
| | - Jinyan Li
- Faculty of Engineering and IT in the University of Technology Sydney
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13
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Vickman RE, Broman MM, Lanman NA, Franco OE, Sudyanti PAG, Ni Y, Ji Y, Helfand BT, Petkewicz J, Paterakos MC, Crawford SE, Ratliff TL, Hayward SW. Heterogeneity of human prostate carcinoma-associated fibroblasts implicates a role for subpopulations in myeloid cell recruitment. Prostate 2020; 80:173-185. [PMID: 31763714 DOI: 10.1002/pros.23929] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/10/2019] [Indexed: 01/01/2023]
Abstract
BACKGROUND Carcinoma-associated fibroblasts (CAF) are a heterogeneous group of cells within the tumor microenvironment (TME) that can promote tumorigenesis in the prostate. By understanding the mechanism(s) by which CAF contributes to tumor growth, new therapeutic targets for the management of this disease may be identified. These studies determined whether unique sub-populations of human prostate CAF can be identified and functionally characterized. METHODS Single-cell RNA-seq of primary human prostate CAF followed by unsupervised clustering was utilized to generate cell clusters based on differentially expressed (DE) gene profiles. Potential communication between CAF and immune cells was analyzed using in vivo tissue recombination by combining CAF or normal prostate fibroblasts (NPF) with non-tumorigenic, initiated prostate epithelial BPH-1 cells. Resultant grafts were assessed for inflammatory cell recruitment. RESULTS Clustering of 3321 CAF allows for visualization of six subpopulations, demonstrating heterogeneity within CAF. Sub-renal capsule recombination assays show that the presence of CAF significantly increases myeloid cell recruitment to resultant tumors. This is supported by significantly increased expression of chemotactic chemokines CCL2 and CXCL12 in large clusters compared to other subpopulations. Bayesian analysis topologies also support differential communication signals between chemokine-related genes of individual clusters. Migration of THP-1 monocyte cells in vitro is stimulated in the presence of CAF conditioned medium (CM) compared with NPF CM. Further in vitro analyses suggest that CAF-derived chemokine CCL2 may be responsible for CAF-stimulated migration of THP-1 cells, since neutralization of this chemokine abrogates migration capacity. CONCLUSIONS CAF clustering based on DE gene expression supports the concept that clusters have unique functions within the TME, including a role in immune/inflammatory cell recruitment. These data suggest that CCL2 produced by CAF may be involved in the recruitment of inflammatory cells, but may also directly regulate the growth of the tumor. Further studies aimed at characterizing the subpopulation(s) of CAF which promote immune cell recruitment to the TME and/or stimulate prostate cancer growth and progression will be pursued.
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Affiliation(s)
- Renee E Vickman
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois
| | - Meaghan M Broman
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana
| | - Nadia A Lanman
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana
- Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana
| | - Omar E Franco
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois
| | | | - Yang Ni
- Department of Statistics, Texas A&M University, College Station, Texas
| | - Yuan Ji
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | - Brian T Helfand
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois
| | | | - Michael C Paterakos
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois
| | - Susan E Crawford
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois
| | - Timothy L Ratliff
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana
- Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana
| | - Simon W Hayward
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois
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14
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Abstract
Reconstructing lineage relationships between cells within a tissue or organism is a long-standing aim in biology. Traditionally, lineage tracing has been achieved through the (genetic) labeling of a cell followed by the tracking of its offspring. Currently, lineage trajectories can also be predicted using single-cell transcriptomics. Although single-cell transcriptomics provides detailed phenotypic information, the predicted lineage trajectories do not necessarily reflect genetic relationships. Recently, techniques have been developed that unite these strategies. In this Review, we discuss transcriptome-based lineage trajectory prediction algorithms, single-cell genetic lineage tracing, and the promising combination of these techniques for stem cell and cancer research.
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Affiliation(s)
- Lennart Kester
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Alexander van Oudenaarden
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands.
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