Translating vibrational spectroscopy into clinical applications – vision or reality?

2016 ◽  
Vol 187 ◽  
pp. 603-607 ◽  
Author(s):  
Wolfgang Petrich
Keyword(s):  
Vibrational Spectroscopy ◽  
Biomedical Applications ◽  
Single Cell Analysis ◽  
Academic Research ◽  
Optical Resolution ◽  
Analysis Data ◽  
Diagnostic Value ◽  
Cell Analysis ◽  
Data Analysis Procedure

The Faraday Discussion meeting “Advanced Vibrational Spectroscopy for Biomedical Applications” provided an excellent opportunity to share and discuss recent research and applications on a highly interdisciplinary level. Spectral pathology, single cell analysis, data handling, clinical spectroscopy, and the spectral analysis of biofluids were among the topics covered during the meeting. The focus on discussion rather than “merely” presentation was highly appreciated and fruitful discussions evolved around the interpretation of the amide-bands, optical resolution, the role of diffraction and data analysis procedure, to name a few. The meeting made clear that the spectroscopy of molecular vibrations in biomolecules has evolved from a purely academic research tool to a technology used in clinical practice in some cases. In this sense, biomedical vibrational spectroscopy has reached a pivotal point at which questions like diagnostic value, therapeutic consequence and financial viability are gaining more and more importance.

scholarly journals Role of Calcium Signaling Pathway-Related Gene Regulatory Networks in Ischemic Stroke Based on Multiple WGCNA and Single-Cell Analysis

2021 ◽  
Vol 2021 ◽  
pp. 1-35
Author(s):  
Weiwei Lin ◽  
Yangxin Wang ◽  
Yisheng Chen ◽  
Qiangwei Wang ◽  
Zhaowen Gu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Calcium Signaling ◽  
Single Cell ◽  
Signaling Pathway ◽  
Single Cell Analysis ◽  
Cell Analysis ◽  
Kegg Pathways ◽  
Calcium Signaling Pathway ◽  
Core Genes

Background. This study is aimed at investigating the changes in relevant pathways and the differential expression of related gene expression after ischemic stroke (IS) at the single-cell level using multiple weighted gene coexpression network analysis (WGCNA) and single-cell analysis. Methods. The transcriptome expression datasets of IS samples and single-cell RNA sequencing (scRNA-seq) profiles of cerebrovascular tissues were obtained by searching the Gene Expression Omnibus (GEO) database. First, gene pathway scoring was calculated via gene set variation analysis (GSVA) and was imported into multiple WGCNA to acquire key pathways and pathway-related hub genes. Furthermore, SCENIC was used to identify transcription factors (TFs) regulating these core genes using scRNA-seq data. Finally, the pseudotemporal trajectory analysis was used to analyse the role of these TFs on various cell types under hypoxic and normoxic conditions. Results. The scores of 186 KEGG pathways were obtained via GSVA using microarray expression profiles of 40 specimens. WGCNA of the KEGG pathways revealed the two following pathways: calcium signaling pathway and neuroactive ligand-receptor interaction pathways. Subsequently, WGCNA of the gene expression matrix of the samples revealed the calcium signaling pathway-related genes (AC079305.10, BCL10, BCL2A1, BRE-AS1, DYNLL2, EREG, and PTGS2) that were identified as core genes via correlation analysis. Furthermore, SCENIC and pseudotemporal analysis revealed JUN, IRF9, ETV5, and PPARA score gene-related TFs. Jun was found to be associated with hypoxia in endothelial cells, whereas Irf9 and Etv5 were identified as astrocyte-specific TFs associated with oxygen concentration in the mouse cerebral cortex. Conclusions. Calcium signaling pathway-related genes (AC079305.10, BCL10, BCL2A1, BRE-AS1, DYNLL2, EREG, and PTGS2) and TFs (JUN, IRF9, ETV5, and PPARA) were identified to play a key role in IS. This study provides a new perspective and basis for investigating the pathogenesis of IS and developing new therapeutic approaches.

Abstract A101: Single-cell analysis reveals the pivotal role of the innate immune compartment in aCTLA-4 antitumor response

2020 ◽  
Author(s):  
Ido Yofe ◽  
Adam Jelinski ◽  
Isabelle Solomon ◽  
Tomer Landsberger ◽  
Marc Robert de Massy ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Innate Immune ◽  
Pivotal Role ◽  
Cell Analysis ◽  
Antitumor Response

scholarly journals The Expression and Prognostic Value of SUMO1-Activating Enzyme Subunit 1 and Its Potential Mechanism in Triple-Negative Breast Cancer

2021 ◽  
Vol 9 ◽  
Author(s):  
Qingshui Wang ◽  
Wenting Zhong ◽  
Lin Deng ◽  
Qili Lin ◽  
Youyu Lin ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cell Cycle ◽  
Protein Expression ◽  
Single Cell ◽  
Prognostic Model ◽  
Triple Negative ◽  
Single Cell Analysis ◽  
Cell Analysis ◽  
Mrna And Protein Expression

Background: Triple-negative breast cancer (TNBC) is the most invasive and metastatic subtype of breast cancer. SUMO1-activating enzyme subunit 1 (SAE1), an E1-activating enzyme, is indispensable for protein SUMOylation. SAE1 has been found to be a relevant biomarker for progression and prognosis in several tumor types. However, the role of SAE1 in TNBC remains to be elucidated.Methods: In the research, the mRNA expression of SAE1 was analyzed via the cancer genome atlas (TCGA) and gene expression omnibus (GEO) database. Cistrome DB Toolkit was used to predict which transcription factors (TFs) are most likely to increase SAE1 expression in TNBC. The correlation between the expression of SAE1 and the methylation of SAE1 or quantity of tumor-infiltrating immune cells was further invested. Single-cell analysis, using CancerSEA, was performed to query which functional states are associated with SAE1 in different cancers in breast cancer at the single-cell level. Next, weighted gene coexpression network (WGCNA) was applied to reveal the highly correlated genes and coexpression networks of SAE1 in TNBC patients, and a prognostic model containing SAE1 and correlated genes was constructed. Finally, we also examined SAE1 protein expression of 207 TNBC tissues using immunohistochemical (IHC) staining.Results: The mRNA and protein expression of SAE1 were increased in TNBC tissues compared with adjacent normal tissues, and the protein expression of SAE1 was significantly associated with overall survival (OS) and disease-free survival (DFS). Correlation analyses revealed that SAE1 expression was positively correlated with forkhead box M1 (FOXM1) TFs and negatively correlated with SAE1 methylation site (cg14042711) level. WGCNA indicated that the genes coexpressed with SAE1 belonged to the green module containing 1,176 genes. Through pathway enrichment analysis of the module, 1,176 genes were found enriched in cell cycle and DNA repair. Single-cell analysis indicated that SAE1 and its coexpression genes were associated with cell cycle, DNA damage, DNA repair, and cell proliferation. Using the LASSO COX regression, a prognostic model including SAE1 and polo-like kinase 1 (PLK1) was built to accurately predict the likelihood of DFS in TNBC patients.Conclusion: In conclusion, we comprehensively analyzed the mRNA and protein expression, prognosis, and interaction genes of SAE1 in TNBC and constructed a prognostic model including SAE1 and PLK1. These results might be important for better understanding of the role of SAE1 in TNBC. In addition, DNA methyltransferase and TFs inhibitor treatments targeting SAE1 might improve the survival of TNBC patients.

scholarly journals Single Cell Analysis Reveals Multiple Requirements for Zinc in the Mammalian Cell Cycle

2019 ◽  
Author(s):  
Maria N. Lo ◽  
Leah J. Damon ◽  
Jian Wei Tay ◽  
Amy E. Palmer
Keyword(s):  
Cell Cycle ◽  
Mammalian Cell ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Genome Integrity ◽  
Cell Analysis ◽  
Fluorescent Reporters ◽  
Cell Cycle Reentry ◽  
Mammalian Cell Cycle

AbstractDespite recognition of the fundamental role of zinc (Zn2+) for growth and proliferation, mechanisms of how Zn2+ deficiency arrests these processes remain enigmatic. We induced subtle intracellular Zn2+ perturbations and tracked asynchronously cycling cells throughout division using fluorescent reporters, high throughput microscopy, and quantitative analysis. We found that Zn2+ deficiency induces quiescence and Zn2+ resupply stimulates cell-cycle reentry. By monitoring single cells after Zn2+ deprivation, we found that depending on where cells were in the cell cycle, they either went quiescent or entered the cell cycle but stalled in S phase. Stalled cells were defective in DNA synthesis and had increased DNA damage levels, suggesting a role for Zn2+ in maintaining genome integrity. Finally, we found that Zn2+ deficiency-induced quiescence does not require the cell-cycle inhibitor p21. Overall, our study provides new insights into when Zn2+ is required during the mammalian cell cycle and the consequences Zn2+ deficiency.

Single cell analysis/data handling: general discussion

2016 ◽  
Vol 187 ◽  
pp. 299-327 ◽  
Author(s):  
Matthew J. Baker ◽  
Royston Goodacre ◽  
Christopher Sammon ◽  
Maria Paula Marques ◽  
Peter Gardner ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Analysis Data ◽  
Data Handling ◽  
Cell Analysis

scholarly journals Single-cell analysis of developing and azoospermia human testicles reveals central role of Sertoli cells

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
LiangYu Zhao ◽  
ChenCheng Yao ◽  
XiaoYu Xing ◽  
Tao Jing ◽  
Peng Li ◽  
...  
Keyword(s):  
Single Cell ◽  
Sertoli Cells ◽  
Single Cell Analysis ◽  
Klinefelter Syndrome ◽  
Diagnostic Methods ◽  
Obstructive Azoospermia ◽  
Cell Analysis ◽  
Y Chromosome Microdeletions ◽  
Healthy Donors

Abstract Clinical efficacy of treatments against non-obstructive azoospermia (NOA), which affects 1% of men, are currently limited by the incomplete understanding of NOA pathogenesis and normal spermatogenic microenvironment. Here, we profile >80,000 human testicular single-cell transcriptomes from 10 healthy donors spanning the range from infant to adult and 7 NOA patients. We show that Sertoli cells, which form the scaffold in the testicular microenvironment, are severely damaged in NOA patients and identify the roadmap of Sertoli cell maturation. Notably, Sertoli cells of patients with congenital causes (Klinefelter syndrome and Y chromosome microdeletions) are mature, but exhibit abnormal immune responses, while the cells in idiopathic NOA (iNOA) are physiologically immature. Furthermore, we find that inhibition of Wnt signaling promotes the maturation of Sertoli cells from iNOA patients, allowing these cells to regain their ability to support germ cell survival. We provide a novel perspective on the development of diagnostic methods and therapeutic targets for NOA.

scholarly journals Optical Fiber Tweezers: A Versatile Tool for Optical Trapping and Manipulation

Micromachines ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 114 ◽  
Author(s):  
Xiaoting Zhao ◽  
Nan Zhao ◽  
Yang Shi ◽  
Hongbao Xin ◽  
Baojun Li
Keyword(s):  
Optical Fiber ◽  
Biomedical Applications ◽  
Optical Trapping ◽  
Single Cell Analysis ◽  
Cell Assembly ◽  
Cell Analysis ◽  
Compact Structure ◽  
Versatile Tool ◽  
Material Sciences ◽  
Significant Attention

Optical trapping is widely used in different areas, ranging from biomedical applications, to physics and material sciences. In recent years, optical fiber tweezers have attracted significant attention in the field of optical trapping due to their flexible manipulation, compact structure, and easy fabrication. As a versatile tool for optical trapping and manipulation, optical fiber tweezers can be used to trap, manipulate, arrange, and assemble tiny objects. Here, we review the optical fiber tweezers-based trapping and manipulation, including dual fiber tweezers for trapping and manipulation, single fiber tweezers for trapping and single cell analysis, optical fiber tweezers for cell assembly, structured optical fiber for enhanced trapping and manipulation, subwavelength optical fiber wire for evanescent fields-based trapping and delivery, and photothermal trapping, assembly, and manipulation.

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