Article
Multidisciplinary Sciences
Hanqing Liu, Jingtian Zhou, Wei Tian, Chongyuan Luo, Anna Bartlett, Andrew Aldridge, Jacinta Lucero, Julia K. Osteen, Joseph R. Nery, Huaming Chen, Angeline Rivkin, Rosa G. Castanon, Ben Clock, Yang Eric Li, Xiaomeng Hou, Olivier B. Poirion, Sebastian Preissl, Antonio Pinto-Duarte, Carolyn O'Connor, Lara Boggeman, Conor Fitzpatrick, Michael Nunn, Eran A. Mukamel, Zhuzhu Zhang, Edward M. Callaway, Bing Ren, Jesse R. Dixon, M. Margarita Behrens, Joseph R. Ecker
Summary: The study comprehensively assessed the epigenomes of different cell types in the mouse brain, revealing the diversity and spatial organization of cell types, as well as the repetitive usage of regulators for distinguishing cell subtypes. By constructing an artificial neural network model, it is possible to accurately predict the cell type and spatial location of individual neurons in the brain.
Article
Chemistry, Analytical
Seungyeop Choi, Insu Park, Sang Hyun Lee, Kang In Yeo, Gyeongjun Min, Sung-Hun Woo, Yoon Suk Kim, Sei Young Lee, Sang Woo Lee
Summary: In this study, a single-cell analysis platform was introduced to continuously measure the electric response in a large number of cells. By using electric frequency and voltage variables, the platform allows for the evaluation of cell electrical phenotyping and identification of different cell types and drug responses.
Article
Biochemistry & Molecular Biology
Mengjie Chen, Qi Zhan, Zepeng Mu, Lili Wang, Zhaohui Zheng, Jinlin Miao, Ping Zhu, Yang Li
Summary: Dmatch is a method for aligning multiple scRNA-seq experiments, leveraging an external expression atlas and kernel density matching to integrate diverse datasets and extract biological insights. The method performs well in simulations and shows great potential when applied to clinical samples, enabling cell type-specific differential gene expression comparisons and revealing shared cell populations.
Article
Cell & Tissue Engineering
Hailong Zheng, Jiajing Xie, Kai Song, Jing Yang, Huiting Xiao, Jiashuai Zhang, Keru Li, Rongqiang Yuan, Yuting Zhao, Yunyan Gu, Wenyuan Zhao
Summary: This study proposes a stemness index for single-cell samples (StemSC) based on relative expression orderings (REO) of gene pairs. The StemSC shows higher negative correlations with differentiation time and can leverage existing experimentally validated stem cells to recognize stem-like cells. The index is robust to batch effect and can be used to identify stem-like tumor cells in independent tumor datasets.
STEM CELL RESEARCH & THERAPY
(2022)
Article
Multidisciplinary Sciences
Michael Rieger, Christian Dellenbach, Johannes vom Berg, Jane Beil-Wagner, Ange Maguy, Stephan Rohr
Summary: The POEMS system is a panoramic opto-electrical measurement and stimulation system that allows flexible combinations of optical and electrical recording and stimulation modalities for investigating cardiac function. Composed of 294 optical fibers and 64 electrodes forming a cup covering the entire ventricular surface of mouse hearts, the system enables straightforward 'drop&go' experimentation.
NATURE COMMUNICATIONS
(2021)
Article
Medicine, Research & Experimental
Mizuki Izawa, Nobuyuki Tanaka, Tetsushi Murakami, Tadatsugu Anno, Yu Teranishi, Kimiharu Takamatsu, Shuji Mikami, Kazuhiro Kakimi, Takeshi Imamura, Kazuhiro Matsumoto, Mototsugu Oya
Summary: This study focuses on the expression of CD73 in bladder cancer patients and reveals its interaction with specific T-cell types and its impact on tumor progression and prognosis. CD73 expression is associated with immunoregulatory functions in specific T cells, providing valuable insights for immunotherapy in bladder cancer.
LABORATORY INVESTIGATION
(2023)
Article
Biochemistry & Molecular Biology
Tudor Groza, Federico Lopez Gomez, Hamed Haseli Mashhadi, Violeta Munoz-Fuentes, Osman Gunes, Robert Wilson, Pilar Cacheiro, Anthony Frost, Piia Keskivali-Bond, Bora Vardal, Aaron McCoy, Tsz Kwan Cheng, Luis Santos, Sara Wells, Damian Smedley, Ann-Marie Mallon, Helen Parkinson
Summary: The International Mouse Phenotyping Consortium (IMPC) website provides a curated and analyzed platform for knockout mouse phenotyping data, which is valuable for molecular diagnosis and gene function research in rare diseases. The data and materials have been widely used in over 4,600 publications, indicating their significance.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Zizhen Yao, Hanqing Liu, Fangming Xie, Stephan Fischer, Ricky S. Adkins, Andrew Aldridge, Seth A. Ament, Anna Bartlett, M. Margarita Behrens, Koen Van den Berge, Darren Bertagnolli, Hector Roux de Bezieux, Tommaso Biancalani, A. Sina Booeshaghi, Hector Corrada Bravo, Tamara Casper, Carlo Colantuoni, Jonathan Crabtree, Heather Creasy, Kirsten Crichton, Megan Crow, Nick Dee, Elizabeth L. Dougherty, Wayne Doyle, Sandrine Dudoit, Rongxin Fang, Victor Felix, Olivia Fong, Michelle Giglio, Jeff Goldy, Mike Hawrylycz, Brian R. Herb, Ronna Hertzano, Xiaomeng Hou, Qiwen Hu, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Yang Eric Li, Jacinta D. Lucero, Chongyuan Luo, Anup Mahurkar, Delissa McMillen, Naeem M. Nadaf, Joseph R. Nery, Thuc Nghi Nguyen, Sheng-Yong Niu, Vasilis Ntranos, Joshua Orvis, Julia K. Osteen, Thanh Pham, Antonio Pinto-Duarte, Olivier Poirion, Sebastian Preissl, Elizabeth Purdom, Christine Rimorin, Davide Risso, Angeline C. Rivkin, Kimberly Smith, Kelly Street, Josef Sulc, Valentine Svensson, Michael Tieu, Amy Torkelson, Herman Tung, Eeshit Dhaval Vaishnav, Charles R. Vanderburg, Cindy van Velthoven, Xinxin Wang, Owen R. White, Z. Josh Huang, Peter Kharchenko, Lior Pachter, John Ngai, Aviv Regev, Bosiljka Tasic, Joshua D. Welch, Jesse Gillis, Evan Z. Macosko, Bing Ren, Joseph R. Ecker, Hongkui Zeng, Eran A. Mukamel
Summary: Using single-cell transcriptomics, this study generated transcriptomes and epigenomes from over 500,000 individual cells in the mouse primary motor cortex, resulting in a reference atlas containing over 56 highly replicable neuronal cell types. They also discovered thousands of concordant marker genes and gene regulatory elements for these cell types.
Article
Chemistry, Analytical
Tao Gao, Songyan Zhao, Junhua Sun, Qiongbo Huang, Shipeng Long, Mingming Lv, Jiehua Ma, Zhigang Guo, Genxi Li
Summary: This study developed a method called aptamer-mounted nest-PCR (Apt-nPCR), allowing quantitative phenotyping of single cells. Aptamers were used as recognition elements to bind antigens and templates for multiplexed and quantitative detection. This method addressed technical challenges in single-cell phenotype analysis and can be used as a complementary method to single-cell genotyping methods.
ANALYTICAL CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Fang Wang, Qihan Wang, Vakul Mohanty, Shaoheng Liang, Jinzhuang Dou, Jincheng Han, Darlan Conterno Minussi, Ruli Gao, Li Ding, Nicholas Navin, Ken Chen
Summary: The MEDALT algorithm and LSA statistical routine accurately infer the evolutionary history of cell populations based on SCCN lineage trees to discover fitness-associated genes. By analyzing data from triple-negative breast cancer patients, essential genes for breast cancer fitness and patient survival can be effectively predicted.
Article
Oncology
Ana Costa, Cecile Thirant, Amira Kramdi, Cecile Pierre-Eugene, Caroline Louis-Brennetot, Orphee Blanchard, Didier Surdez, Nadege Gruel, Eve Lapouble, Gaelle Pierron, Deborah Sitbon, Herve Brisse, Arnaud Gauthier, Paul Freneaux, Mylene Bohec, Virginie Raynal, Sylvain Baulande, Renaud Leclere, Gabriel Champenois, Andre Nicolas, Didier Meseure, Angela Bellini, Aurelien Marabelle, Birgit Geoerger, Fatima Mechta-Grigoriou, Gudrun Schleiermacher, Laurie Menger, Olivier Delattre, Isabelle Janoueix-Lerosey
Summary: This study reveals that the immunocompromised microenvironment of neuroblastoma tumors is characterized by dysfunctional T cells and accumulation of immunosuppressive cells. The study provides a new and valuable data resource to better understand the neuroblastoma ecosystem and suggests novel therapeutic strategies targeting both tumor cells and components of the microenvironment.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Engineering, Biomedical
Xi Zhao, Zixun Wang, Xianglin Ji, Shuyu Bu, Peilin Fang, Yuan Wang, Mingxue Wang, Yang Yang, Wenjun Zhang, Anskar Y. H. Leung, Peng Shi
Summary: This study presents a nanoneedle-based discrete single-cell miRNA profiling technique for convenient, sensitive, and efficient analysis of AML heterogeneity. The technique allows simultaneous analysis of multiple miRNAs in a large number of living AML cells, providing multidimensional analysis of AML subtypes for prognostic and therapeutic decision-making.
Article
Chemistry, Analytical
Peixian Li, Ye Ai
Summary: Biophysical markers of cells have shown promise in studying, characterizing, and classifying different cell types. The lack of cell sorting ability based on multivariate biophysical markers presents a challenge in isolating specific cell types. This study demonstrates label-free and high-throughput acoustic single-cell sorting activated by the characterization of multivariate biophysical phenotypes, providing a solution to the challenges of cell purification without specific molecular biomarkers.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Michele Bortolomeazzi, Lucia Montorsi, Damjan Temelkovski, Mohamed Reda Keddar, Amelia Acha-Sagredo, Michael J. Pitcher, Gianluca Basso, Luigi Laghi, Manuel Rodriguez-Justo, Jo Spencer, Francesca D. Ciccarelli
Summary: SIMPLI is a flexible and technology-agnostic software for multiplexed imaging data analysis, allowing single-cell analysis and quantification of marker expression while preserving spatial information. Its customizability and parallel processing capabilities make it suitable for large datasets.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Masanobu Iwanaga, Takashi Hironaka, Naoki Ikeda, Takehito Sugasawa, Kazuhiro Takekoshi
Summary: This study demonstrates that highly fluorescence-enhancing all-dielectric metasurface biosensors can detect single-target cell-free DNA (cfDNA) specific to human practice effect. By combining metasurface biosensors with a reduced-cycle polymerase chain reaction (PCR) technique, high-precision detection of cfDNA was achieved. The results showed that the metasurface biosensors can successfully discriminate the target from zero at a single-molecule concentration with high statistical confidence.
Article
Biophysics
Yang Zhao, Ke Wang, Deyong Chen, Beiyuan Fan, Ying Xu, Yifei Ye, Junbo Wang, Jian Chen, Chengjun Huang
BIOSENSORS & BIOELECTRONICS
(2018)
Article
Nanoscience & Nanotechnology
Yifei Ye, Yang Zhao, Jie Cheng, Mingxiao Li, Chengjun Huang
MICRO & NANO LETTERS
(2018)
Article
Genetics & Heredity
Hu-He Chao, Lin Li, Xiao Gao, Chengrong Wang, Wentao Yue
Review
Chemistry, Analytical
Jie Cheng, Yang Liu, Yang Zhao, Lina Zhang, Lingqian Zhang, Haiyang Mao, Chengjun Huang
Article
Chemistry, Analytical
Yifei Ye, Xiaofeng Luan, Lingqian Zhang, Wenjie Zhao, Jie Cheng, Mingxiao Li, Yang Zhao, Chengjun Huang
Article
Public, Environmental & Occupational Health
Wentao Yue, Enjie Zhang, Ruixia Liu, Yue Zhang, Chengrong Wang, Shen Gao, Shaofei Su, Xiao Gao, Qingqing Wu, Xiaokui Yang, Aris T. Papageorghiou, Chenghong Yin
Summary: The China Birth Cohort Study is a national study aiming to investigate risk factors for birth defects and develop strategies for their reduction. The study has completed two phases of recruitment and has collected biological samples from participants. The study aims to recruit 500,000 participants by December 2021.
EUROPEAN JOURNAL OF EPIDEMIOLOGY
(2022)
Article
Cell Biology
Hongyu Zhao, Yan Gao, Jinwei Miao, Suwen Chen, Jie Li, Zhefeng Li, Chenghong Yin, Wentao Yue
Summary: The study explored the heterogeneity of ovarian cancer through single-cell RNA-seq and identified a subtype associated with poor survival and clinical response. Utilizing specific gene profiles, four phenotypes with different survival and response to immunotherapy were identified, advancing the understanding of OC pathogenesis and leading to promising therapeutic strategies.
CELL DEATH & DISEASE
(2021)
Article
Chemistry, Analytical
Xiaofeng Luan, Yuang Li, Haiping Zhao, Sheng Sun, Yuanyuan Fan, Wenchang Zhang, Lingqian Zhang, Mingxiao Li, Jinghui Wang, Tian Zhi, Lina Zhang, Yang Zhao, Chengjun Huang
Summary: This study proposes a toolchain for enriching and proliferating single cells from pleural effusions and characterizing their adherent morphologies and suspended electrical properties. The results reveal a significant correlation between the adherent morphology and suspended electrical properties of single cells.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Chemistry, Analytical
Yijun Zhang, Yuang Li, Xiaofeng Luan, Xin Li, Jiahong Jiang, Yuanyuan Fan, Mingxiao Li, Chengjun Huang, Lingqian Zhang, Yang Zhao
Summary: Point-of-care testing (POCT) techniques based on microfluidic devices are becoming increasingly important in public health. This paper proposes a 3D capillary-driven multi-microporous membrane-based trigger valve to address the issues of existing 2D valves. The results show that the 3D valve has a high gating threshold, high trigger efficiency, and can perform multi-step operations.
Article
Medicine, Research & Experimental
Jiahao Guo, Xiaoyang Han, Jie Li, Zhefeng Li, Junjie Yi, Yan Gao, Xiaoting Zhao, Wentao Yue
Summary: By integrating single-cell sequencing data, researchers discovered a cell subcluster closely associated with metastasis in ovarian cancer and identified RAB13 as its key marker. Experimental results showed that downregulation of RAB13 expression can reduce migration and invasion of ovarian cancer cells, and several potential drugs that may inhibit RAB13 were predicted. This study provides new insights and potential therapeutic targets for the research on ovarian cancer metastasis.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Nanoscience & Nanotechnology
Xiaofeng Luan, Pengbin Liu, Di Huang, Haiping Zhao, Yuang Li, Sheng Sun, Wenchang Zhang, Lingqian Zhang, Mingxiao Li, Tian Zhi, Yang Zhao, Chengjun Huang
Summary: Real-time transformation is crucial for impedance flow cytometry in practice, but the translation of raw data to cellular intrinsic electrical properties is time-consuming. We proposed a fast parallel physical fitting solver that characterizes single cells' electrical properties within 0.62 ms/cell. Based on this solver, we implemented physics-informed real-time impedance flow cytometry (piRT-IFC), which showed comparable speed but higher accuracy than the fully connected neural network predictor. In addition, we demonstrated the advantages of piRT-IFC in handling unfamiliar samples without pretraining.
MICROSYSTEMS & NANOENGINEERING
(2023)
Article
Nanoscience & Nanotechnology
Yuang Li, Xue Li, Lina Zhang, Xiaofeng Luan, Jiahong Jiang, Lingqian Zhang, Mingxiao Li, Jinghui Wang, Jiangang Duan, Haiping Zhao, Yang Zhao, Chengjun Huang
Summary: Inspired by the teapot effect, a tap-triggered self-wetting strategy was proposed and applied to a 3D sieve for filtering rare cells. The results showed that this strategy significantly improved the performance of passive microparticle filtration.
MICROSYSTEMS & NANOENGINEERING
(2023)
Article
Engineering, Biomedical
Jie Cheng, Lina Zhang, Yiran Zhang, Yifei Ye, Wenjie Zhao, Lingqian Zhang, Yuang Li, Yang Liu, Wenchang Zhang, Hongyan Guo, Mingxiao Li, Yang Zhao, Chengjun Huang
Summary: In this paper, a three-dimensional sieving method for rare tumor cell enrichment was proposed. It effectively eliminated dead zones in traditional two-dimensional cell filters, resulting in high throughput and recovery rates. The method was able to effectively enrich rare target cells from pleural effusion samples and the purified cells exhibited significantly stronger proliferation capabilities compared to unprocessed cells.
BIO-DESIGN AND MANUFACTURING
(2022)
Article
Biotechnology & Applied Microbiology
Meng Ren, Yan Gao, Qi Chen, Hongyu Zhao, Xiaoting Zhao, Wentao Yue
BIOMED RESEARCH INTERNATIONAL
(2020)
Article
Chemistry, Analytical
Yi Zhang, Yang Zhao, Deyong Chen, Ke Wang, Yuanchen Wei, Ying Xu, Chengjun Huang, Junbo Wang, Jian Chen
