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Liu YC, Ansaryan S, Tan J, Broguiere N, Lorenzo-Martín LF, Homicsko K, Coukos G, Lütolf MP, Altug H. Nanoplasmonic Single-Tumoroid Microarray for Real-Time Secretion Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401539. [PMID: 38924371 DOI: 10.1002/advs.202401539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/30/2024] [Indexed: 06/28/2024]
Abstract
Organoid tumor models have emerged as a powerful tool in the fields of biology and medicine as such 3D structures grown from tumor cells recapitulate better tumor characteristics, making these tumoroids unique for personalized cancer research. Assessment of their functional behavior, particularly protein secretion, is of significant importance to provide comprehensive insights. Here, a label-free spectroscopic imaging platform is presented with advanced integrated optofluidic nanoplasmonic biosensor that enables real-time secretion analysis from single tumoroids. A novel two-layer microwell design isolates tumoroids, preventing signal interference, and the microarray configuration allows concurrent analysis of multiple tumoroids. The dual imaging capability combining time-lapse plasmonic spectroscopy and bright-field microscopy facilitates simultaneous observation of secretion dynamics, motility, and morphology. The integrated biosensor is demonstrated with colorectal tumoroids derived from both cell lines and patient samples to investigate their vascular endothelial growth factor A (VEGF-A) secretion, growth, and movement under various conditions, including normoxia, hypoxia, and drug treatment. This platform, by offering a label-free approach with nanophotonics to monitor tumoroids, can pave the way for new applications in fundamental biological studies, drug screening, and the development of therapies.
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Affiliation(s)
- Yen-Cheng Liu
- Bionanophotonic Systems Laboratory, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Saeid Ansaryan
- Bionanophotonic Systems Laboratory, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Jiayi Tan
- Bionanophotonic Systems Laboratory, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Nicolas Broguiere
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Luis Francisco Lorenzo-Martín
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Krisztian Homicsko
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Rue du Bugnon 46, Lausanne, 1005, Switzerland
- Ludwig Institute for Cancer Research, Ludwig Lausanne Branch, Chem. des Boveresses 155, Epalinges, 1066, Switzerland
- Swiss Cancer Center Leman, Rue du Bugnon 25A, Lausanne, 1011, Switzerland
- Agora Translational Research Center, Rue du Bugnon 25A, Lausanne, 1011, Switzerland
| | - George Coukos
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Rue du Bugnon 46, Lausanne, 1005, Switzerland
- Ludwig Institute for Cancer Research, Ludwig Lausanne Branch, Chem. des Boveresses 155, Epalinges, 1066, Switzerland
- Swiss Cancer Center Leman, Rue du Bugnon 25A, Lausanne, 1011, Switzerland
- Agora Translational Research Center, Rue du Bugnon 25A, Lausanne, 1011, Switzerland
| | - Matthias P Lütolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Hatice Altug
- Bionanophotonic Systems Laboratory, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
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Kang W, Hu J, Zhao Q, Song F. Identification of an Autophagy-Related Risk Signature Correlates With Immunophenotype and Predicts Immune Checkpoint Blockade Efficacy of Neuroblastoma. Front Cell Dev Biol 2021; 9:731380. [PMID: 34746127 PMCID: PMC8567030 DOI: 10.3389/fcell.2021.731380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022] Open
Abstract
Neuroblastoma is one of the malignant solid tumors with the highest mortality in childhood. Targeted immunotherapy still cannot achieve satisfactory results due to heterogeneity and tolerance. Exploring markers related to prognosis and evaluating the immune microenvironment remain the major obstacles. Herein, we constructed an autophagy-related gene (ATG) risk model by multivariate Cox regression and least absolute shrinkage and selection operator regression, and identified four prognostic ATGs (BIRC5, GRID2, HK2, and RNASEL) in the training cohort, then verified the signature in the internal and external validation cohorts. BIRC5 and HK2 showed higher expression in MYCN amplified cell lines and tumor tissues consistently, whereas GRID2 and RNASEL showed the opposite trends. The correlation between the signature and clinicopathological parameters was further analyzed and showing consistency. A prognostic nomogram using risk score, International Neuroblastoma Staging System stage, age, and MYCN status was built subsequently, and the area under curves, net reclassification improvement, and integrated discrimination improvement showed more satisfactory prognostic predicting performance. The ATG prognostic signature itself can significantly divide patients with neuroblastoma into high- and low-risk groups; differentially expressed genes between the two groups were enriched in autophagy-related behaviors and immune cell reactions in gene set enrichment analysis (false discovery rate q -value < 0.05). Furthermore, we evaluated the relationship of the signature risk score with immune cell infiltration and the cancer-immunity cycle. The low-risk group was characterized by more abundant expression of chemokines and higher immune checkpoints (PDL1, PD1, CTLA-4, and IDO1). The risk score was significantly correlated with the proportions of CD8+ T cells, CD4+ memory resting T cells, follicular helper T cells, memory B cells, plasma cells, and M2 macrophages in tumor tissues. In conclusion, we developed and validated an autophagy-related signature that can accurately predict the prognosis, which might be meaningful to understand the immune microenvironment and guide immune checkpoint blockade.
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Affiliation(s)
- Wenjuan Kang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jiajian Hu
- Tianjin Key Laboratory of Cancer Prevention and Therapy, Department of Pediatric Oncology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Qiang Zhao
- Tianjin Key Laboratory of Cancer Prevention and Therapy, Department of Pediatric Oncology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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Pillon MC, Gordon J, Frazier MN, Stanley RE. HEPN RNases - an emerging class of functionally distinct RNA processing and degradation enzymes. Crit Rev Biochem Mol Biol 2021; 56:88-108. [PMID: 33349060 PMCID: PMC7856873 DOI: 10.1080/10409238.2020.1856769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding) RNases are an emerging class of functionally diverse RNA processing and degradation enzymes. Members are defined by a small α-helical bundle encompassing a short consensus RNase motif. HEPN dimerization is a universal requirement for RNase activation as the conserved RNase motifs are precisely positioned at the dimer interface to form a composite catalytic center. While the core HEPN fold is conserved, the organization surrounding the HEPN dimer can support large structural deviations that contribute to their specialized functions. HEPN RNases are conserved throughout evolution and include bacterial HEPN RNases such as CRISPR-Cas and toxin-antitoxin associated nucleases, as well as eukaryotic HEPN RNases that adopt large multi-component machines. Here we summarize the canonical elements of the growing HEPN RNase family and identify molecular features that influence RNase function and regulation. We explore similarities and differences between members of the HEPN RNase family and describe the current mechanisms for HEPN RNase activation and inhibition.
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Affiliation(s)
- Monica C. Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jacob Gordon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Meredith N. Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E. Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
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Kumar S, Matthews QL, Sims B. Effects of Cocaine on Human Glial-Derived Extracellular Vesicles. Front Cell Dev Biol 2021; 8:563441. [PMID: 33505956 PMCID: PMC7830252 DOI: 10.3389/fcell.2020.563441] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Microglia are important myeloid cells present in the brain parenchyma that serve a surveillance function in the central nervous system. Microglial cell activation results in neuroinflammation that, when prolonged, can disrupt immune homeostasis and neurogenesis. Activated microglia-derived extracellular vesicles (EVs) may be involved in the propagation of inflammatory responses and modulation of cell-to-cell communication. However, a complete understanding of how EVs are regulated by drugs of abuse, such as cocaine, is still lacking. FINDINGS Cocaine exposure reduced human microglial cell (HMC3) viability, decreased expression of CD63 and dectin-1 in HMC3-derived EVs, and increased expression of the apoptotic marker histone H2A.x in HMC3-derived EVs. CONCLUSION Cocaine impacts HMC3 cell viability and specific EV protein expression, which could disrupt cellular signaling and cell-to-cell communication.
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Affiliation(s)
- Sanjay Kumar
- Department of Pediatrics/Division of Neonatology and Center of Glial Biology in Medicine at the University of Alabama School of Medicine, University of Alabama, Birmingham, AL, United States
| | - Qiana L. Matthews
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL, United States
| | - Brian Sims
- Department of Pediatrics/Division of Neonatology and Center of Glial Biology in Medicine at the University of Alabama School of Medicine, University of Alabama, Birmingham, AL, United States
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