Article
Multidisciplinary Sciences
Erwin M. Schoof, Benjamin Furtwangler, Nil Uresin, Nicolas Rapin, Simonas Savickas, Coline Gentil, Eric Lechman, Ulrich auf Dem Keller, John E. Dick, Bo T. Porse
Summary: The study demonstrates a comprehensive experimental and computational workflow that establishes global single-cell mass spectrometry-based proteomics as a tool for large-scale single-cell analyses, enabling the exploration of cellular heterogeneity. The approach presented is capable of consistently quantifying around 1000 proteins per cell within limited instrument time.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Tahereh Khajvand, Peifeng Huang, Linmei Li, Mingxia Zhang, Fengjiao Zhu, Xing Xu, Mengjiao Huang, Chaoyong Yang, Yao Lu, Zhi Zhu
Summary: This study introduces an integrated droplet microfluidic device for multiplexed single-cell secretion analysis, which can effectively capture and detect protein secretion heterogeneity among cells.
Article
Chemistry, Multidisciplinary
Qi Wu, Peiling Dai, Yun Wang, Jin Zhang, Meng Li, Kenneth Yin Zhang, Shujuan Liu, Wei Huang, Qiang Zhao
Summary: This study introduces a polymeric luminescent probe composed of two luminophores with significantly different luminescence lifetimes for time-resolved independent analysis. A four-dimensional relationship model was established to analyze the luminescence intensity, fluorescence/phosphorescence ratio, hypochlorite concentration, and oxygen content. In cellular imaging, independent fluorescence response to hypochlorite and phosphorescence response to oxygen were clearly demonstrated in separated time intervals. This work offers a new approach for the development of multiplex biosensing and bioimaging.
Article
Genetics & Heredity
Jianjun Huang, Li Liu, Lingling Qin, Hehua Huang, Xue Li
Summary: This study utilized single-cell transcriptomics to reveal cellular heterogeneity and identified the importance of endothelial cells in Parkinson's disease (PD). Five upregulated marker genes of endothelial cells were identified as potential therapeutic targets for PD.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Jian Zhou, Olga G. Troyanskaya
Summary: The development of a 'linearly interpretable' framework for analyzing single-cell omics data improves data representation, visualization, and structure discovery in a way that is both interpretable and transferable across datasets.
Article
Cell Biology
Chungmin Han, Hyejin Kang, Johan Yi, Minsu Kang, Hyunjin Lee, Yongmin Kwon, Jaehun Jung, Jingeol Lee, Jaesung Park
Summary: This study introduces a single vesicle analysis method that visualizes marker expressions of individual EVs and investigates their subpopulations. The analysis successfully illustrated the diversity of EVs and revealed distinct patterns of tetraspanin expressions. Application of the analysis demonstrated similarities and dissimilarities between EV fractions acquired from different conventional isolation methods.
JOURNAL OF EXTRACELLULAR VESICLES
(2021)
Article
Immunology
Avishay Dolitzky, Guy Shapira, Sharon Grisaru-Tal, Inbal Hazut, Shmulik Avlas, Yaara Gordon, Micahl Itan, Noam Shomron, Ariel Munitz
Summary: Eosinophils are multifunctional leukocytes involved in regulating tissue homeostasis, host defense, and cancer responses. They can respond to both Type 1 and Type 2 inflammatory stimuli based on recent RNA sequencing data, exhibiting distinct transcription profiles. These findings suggest that eosinophils exhibit heterogeneity and transcriptional differences between Type 1 and Type 2 cells, influencing their diverse activities in various disease settings.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biology
Lixia Pan, Wai Lim Ku, Qingsong Tang, Yaqiang Cao, Keji Zhao
Summary: Cell-to-cell variation in gene expression is a widespread phenomenon that plays important roles in cellular differentiation, function, and disease development. This study presents a technique called scPCOR-seq, which allows simultaneous profiling of chromatin occupancy and RNA expression in the same cell. The technique was successfully applied to analyze chromatin protein binding or histone modification marks and RNA expression in a mixture of human cells, as well as in the differentiation of erythrocyte precursor cells.
COMMUNICATIONS BIOLOGY
(2022)
Article
Dentistry, Oral Surgery & Medicine
Qi-Wen Man, Rui-Fang Li, Jian-Feng Liu, Yi Zhao, Bing Liu
Summary: This study provides insights into the immune ecosystem of odontogenic keratocyst (OKC) and highlights the chemotactic effects of chemokine-enriched myofibroblasts within OKCs. The close interaction between immune cells and fibroblasts demonstrated in this study may be responsible for the osteoclastogenic effects of OKC fibroblasts.
Article
Genetics & Heredity
Chen Zhang, Xueshuai Han, Jingkun Liu, Lei Chen, Ying Lei, Kunying Chen, Jia Si, Tian-yi Wang, Hui Zhou, Xiaoyun Zhao, Xiaohui Zhang, Yihua An, Yueying Li, Qian-Fei Wang
Summary: By single-cell RNA sequencing, this study identified five distinct subpopulations of ex vivo-expanded mesenchymal stem cells (MSCs). Among them, a stem-like subpopulation exhibited strong proliferation and stemness signatures, while another subpopulation of prechondrocytes played a role in immunoregulation. These findings contribute to a better understanding and application of MSCs.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Oncology
Shuyu Wang, Dali Xu, Bo Gao, Shuhan Yan, Yiwei Sun, Xinxing Tang, Yanjia Jiao, Shan Huang, Shumei Zhang
Summary: Bladder cancer is a highly complex and heterogeneous malignancy. This study explored specific molecular subtypes based on DNA methylation status and identified subtype-specific characteristics. The results provide important reference for clinicians to make treatment decisions.
FRONTIERS IN ONCOLOGY
(2022)
Article
Chemistry, Physical
Fangteng Song, Chao Wang, Chunhua Wang, Jianbo Wang, Yu Wu, Yihe Wang, Hong Liu, Yu Zhang, Lin Han
Summary: This study developed an integrated microfluidic platform for the multiplexed outline of exosome secretion by single cells, exploring intercellular heterogeneity and identifying unique secretion patterns in different cell subsets.
Article
Cell & Tissue Engineering
Haoteng Yan, Jiali Zhu, Yanyan Ping, Min Yan, Gaoming Liao, Huating Yuan, Yao Zhou, Fengyu Xiang, Bo Pang, Jinyuan Xu, Lin Pang
Summary: In this study, single-cell transcriptome sequencing data of 6 GBM cohorts were used to identify primary GSCs and characterize their cell states. Two recurrent GSCs subpopulations, pGSCs and qGSCs, were identified based on their cell cycle activity. The processes of tumor development were traced and it was found that GSCs accumulated throughout the whole period, with pGSCs mainly contributing to the early stage and qGSCs enriched in the later stage. Furthermore, an 8-gene prognostic signature reflecting pGSCs activity was constructed and associated with poor clinical outcomes.
Article
Cell & Tissue Engineering
Sergi Beneyto-Calabuig, Anne Kathrin Merbach, Jonas-Alexander Kniffka, Magdalena Antes, Chelsea Szu-Tu, Christian Rohde, Alexander Waclawiczek, Patrick Stelmach, Sarah Graessle, Philip Pervan, Maike Janssen, Jonathan J. M. Landry, Vladimir Benes, Anna Jauch, Michaela Brough, Marcus Bauer, Birgit Besenbeck, Julia Felden, Sebastian Baeumer, Michael Hundemer, Tim Sauer, Caroline Pabst, Claudia Wickenhauser, Linus Angenendt, Christoph Schliemann, Andreas Trumpp, Simon Haas, Michael Scherer, Simon Raffel, Carsten Mueller-Tidow, Lars Velten
Summary: By using the CloneTracer method, researchers discovered that the stem cell compartment in AML patients is mainly composed of healthy and preleukemic cells, while active leukemic stem cells resemble healthy cells in erythroid differentiation. However, abnormal gene expression and differentiation state in myeloid progenitor cells have a significant impact on chemotherapy response and the ability of leukemia cells to differentiate into normal monocytes. The CloneTracer method also has the potential to identify surface markers that are specifically misregulated in leukemic cells. In summary, CloneTracer reveals a differentiation landscape in AML that mimics its healthy counterpart and may determine the biology and therapy response of AML.
Review
Chemistry, Multidisciplinary
Jiaxin Hu, Yanfei Liu, Yimin Du, Xingxing Peng, Zhenbao Liu
Summary: Organelles have been developed as drug carriers, offering advantages in drug loading efficiency and therapeutic effect enhancement. This review summarizes the biogenesis, isolation, and drug-loading methods of four types of organelles, and highlights their potential as drug-delivery systems for disease treatment.
JOURNAL OF CONTROLLED RELEASE
(2023)
Article
Biotechnology & Applied Microbiology
O. M. Chepurna, A. Yakovliev, R. Ziniuk, O. A. Nikolaeva, S. M. Levchenko, H. Xu, M. Y. Losytskyy, J. L. Bricks, Yu L. Slominskii, L. O. Vretik, J. Qu, T. Y. Ohulchanskyy
JOURNAL OF NANOBIOTECHNOLOGY
(2020)
Review
Chemistry, Analytical
Artem Pliss, Paras N. Prasad
METHODS AND APPLICATIONS IN FLUORESCENCE
(2020)
Article
Nanoscience & Nanotechnology
Ting Zhou, Artem Pliss, Yu Chen, Andrey N. Kuzmin, Paras N. Prasad, Junle Qu
NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE
(2020)
Article
Chemistry, Multidisciplinary
Julia C. Bulmahn, Gleb Tikhonowski, Anton A. Popov, Andrey Kuzmin, Sergey M. Klimentov, Andrei Kabashin, Paras N. Prasad
Article
Chemistry, Multidisciplinary
Liang Hong, Artem M. Pliss, Ye Zhan, Wenhan Zheng, Jun Xia, Liwei Liu, Junle Qu, Paras N. Prasad
Article
Multidisciplinary Sciences
Adrian Lita, Artem Pliss, Andrey Kuzmin, Tomohiro Yamasaki, Lumin Zhang, Tyrone Dowdy, Christina Burks, Natalia de Val, Orieta Celiku, Victor Ruiz-Rodado, Elena-Raluca Nicoli, Michael Kruhlak, Thorkell Andresson, Sudipto Das, Chunzhang Yang, Rebecca Schmitt, Christel Herold-Mende, Mark R. Gilbert, Paras N. Prasad, Mioara Larion
Summary: This study reveals that IDH1(mut) results in an increase in monounsaturated fatty acids and their phospholipids in the endoplasmic reticulum, leading to Golgi and ER dilation. Inhibition of IDH1 mutation or SCD silencing restores ER and Golgi morphology, while D-2HG and oleic acid induces morphological defects in these organelles. Moreover, the overexpression of SCD induced by IDH1(mut) rearranges the distribution of lipids in the organelles of glioma cells, contributing to potential therapeutic implications.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Artem Pliss, Andrey N. Kuzmin, Adrian Lita, Rahul Kumar, Orieta Celiku, G. Ekin Atilla-Gokcumen, Omer Gokcumen, Dhyan Chandra, Mioara Larion, Paras N. Prasad
Summary: The Ramanomics platform enables molecular profiling of single organelles in live-cell environments using confocal Raman microspectrometry and biomolecular component analysis algorithms. Significant variations in organellar composition between different cell lines have been discovered, and Ramanomics has been proven effective in identifying diseased cells and revealing large-scale molecular transformations accompanying disease development in organelles.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Artem Pliss, Andrey N. Kuzmin, Paras N. Prasad, Supriya D. Mahajan
Summary: The SARS-CoV-2 virus can cause neurological conditions by invading the nervous system. The dysfunction of mitochondria in brain microglia cells is believed to play a role in the neuropathology of SARS-CoV-2. Using Raman microspectrometry, researchers found that infected microglia cells exhibited reduced mtDNA content and increased phospholipid saturation levels in mitochondria. These changes may be linked to increased synthesis of reactive oxygen species in the organelles.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Optics
Svitlana M. Levchenko, Artem Pliss, Xiao Peng, Paras N. Prasad, Junle Qu
Summary: Fluorescence lifetime imaging (FLIM) is proposed for studying genomic structure, including DNA compaction, replication, and gene expression monitoring. The FLIM assay utilizes two independent mechanisms to sense DNA compaction, which were validated in cultured cells. The obtained data reveal significant differences in compaction between gene-rich and gene-poor pools of genomic DNA.
LIGHT-SCIENCE & APPLICATIONS
(2021)
Article
Optics
Soumik Siddhanta, Andrey N. Kuzmin, Artem Pliss, Alexander S. Baev, Sunil K. Khare, Pramit K. Chowdhury, Ashok K. Ganguli, Paras N. Prasad
Summary: This review provides a historical account of the evolution of Raman spectroscopy and discusses advancements that have allowed for the detection of single molecules and non-invasive analysis of organelles. It addresses the need for a consolidated overview of Raman spectroscopy's broad applications in biosensing, from fundamental biology to disease identification, drug screening, and quality control in food and agriculture. The review also highlights the convergence of Raman spectroscopy with bioanalysis, agriculture, and food quality control, and explores the potential of combining advanced spectroscopy with machine-learning algorithms to establish a new field known as Ramanomics. Future needs and opportunities are also discussed.
ADVANCES IN OPTICS AND PHOTONICS
(2023)
Article
Nanoscience & Nanotechnology
Micah Raab, Artiom Skripka, Julia Bulmahn, Artem Pliss, Andrey Kuzmin, Fiorenzo Vetrone, Paras Prasad
Summary: In this study, we synthesized multi-shell rare-earth doped nanoparticles and achieved independent control in NIR imaging and therapeutic action by using different excitation wavelengths. By generating downshifting emission upon 800 nm excitation and upconversion emission upon 980 nm irradiation, high-contrast NIR imaging in NIR-IIb of optical transparency and selective activation of the surface-bound photosensitizer RB for safer and more specific therapy were achieved.
ACS APPLIED BIO MATERIALS
(2022)
Proceedings Paper
Engineering, Electrical & Electronic
C. -K. Lim, A. A. Popov, G. Tselikov, J. Heo, A. Pliss, S. Kim, A. V. Kabashin, P. N. Prasad
SYNTHESIS AND PHOTONICS OF NANOSCALE MATERIALS XVI
(2019)
