Yanxiang Deng

2023 Regional Award Winner — Post-Doc

Yanxiang Deng

Current Position:
Assistant Professor of Pathology and Laboratory Medicine

University of Pennsylvania (previously, Yale University)

Biomedical Engineering & Biotechnology

Recognized for: Developing a novel microfluidic method for “spatial-omics” to profile the expression of RNA, proteins, and epigenetic markers across spatially organized groups of cells in tissues. Deng’s work has allowed us to construct a map of how RNA, proteins, and epigenetic markers are expressed across groups of cells with respect to cells’ relative positions. This work provides critical insight into how cells in different regions change their behavior during processes like development and disease.

Areas of Research Interest and Expertise: Spatial omics, Single-cell analysis, Microfluidics 

Previous Positions: 

  • BS, Changsha University of Science and Technology, China (Advisor: Yucai Zhou)
  • MS, Huazhong University of Science and Technology, China (Advisor: Zixue Luo, Huaichun Zhou)
  • PhD, Rensselaer Polytechnic Institute (Advisor: Aram Chung)
  • Postdoctoral Associate, Yale University (Advisor: Rong Fan)

Research Summary:

In multicellular organisms, like humans, birds, and fish, single cells act collectively to form complex structures and tissues. The function of these tissues is dependent on individual cells performing unique functions based on their location in the tissue and what other cells are nearby. Current advances in single-cell profiling techniques have provided an unprecedented amount of information about the behaviors of individual cells, but these techniques overlook a crucial dimension, space! Without this information, it’s impossible to relate cellular function to location.

Yanxiang Deng, PhD combines engineering and high-throughput cell profiling to understand how cells behave relative to their location in a complex tissue. By designing a specialized microfluidic device, Deng can deliver molecular barcodes to individual cells in a fixed tissue sample with incredible precision. These barcodes allow us to construct a map of the cells and their position within the tissue. Deng has combined this technique with cellular profiling technologies to capture spatially resolved information about gene and protein expression, and information about the chromatin states across the genome. The state of chromatin, which is a mixture of histone proteins and DNA, in part, determines which genes are expressed. This suite of tools is referred to as “spatial-omics.” Deng pioneered the development of spatial-omics tools that allowed scientists to extract one layer of information, gene expression or chromatin states. Deng has further developed two spatial multi-omics tools to allow for joint mapping of chromatin accessibility and gene expression or histone modifications and gene expression.

This work gives us novel insight into how the behavior of individual cells is regulated and differentiated based on their local environment.

“This recognition gives me the confidence to pioneer and engender novel and powerful technologies. These technologies will greatly improve our ability to study tissue complexity and reveal the salient features of tissue architecture in physiology and disease.”

Key Publications:

  1. D. Zhang, Y. Deng, P. Kukanja, E. Agirre, M. Bartosovic, M. Dong, C. Ma, S. Ma, G. Su, S. Bao, Y. Liu, Y. Xiao, G.B. Rosoklija, A.J. Dwork, J.J. Mann, K.W. Leong, M. Boldrini, L. Wang, M. Haeussler, B.J. Raphael, Y. Kulger, G. Castelo-Branco, and R. Fan. Spatially resolved epigenome-transcriptome co-profiling of mammalian tissues at the cellular level. Nature. 2023.
  2. Y. Deng, M. Bartosovic, P. Kukanja, D. Zhang, Y. Liu, G. Su, A. Enninful, Z. Bai, G. Castelo-Branco, and R. Fan. Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. Science. 2022.
  3. Y. Deng, M. Bartosovic, S. Ma, D. Zhang, P. Kukanja, Y. Xiao, G. Su, Y. Liu, X. Qin, G.B. Rosoklija, A.J. Dwork, J.J. Mann, M.L. Xu, S. Halene, J.E. Craft, K.W. Leong, M. Boldrini, G. Castelo-Branco, and R. Fan. Spatial profiling of chromatin accessibility in mouse and human tissues. Nature. 2022.
  4. Y. Liu, M. Yang, Y. Deng, G. Su, A. Enninful, C.G. Guo, T. Tebaldi, D. Zhang, D. Kim, Z. Bai, E. Norris, A. Pan, J. Li, Y. Xiao, S. Halene, and R. Fan. High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. Cell. 2020.

Other Honors:

2015Founders Award of Excellence, Rensselaer Polytechnic Institute
2009Honor student of Humana Province, China
2008National Scholarship, China


In the Media:

Nature Reviews Genetics, Research HighlightLayering epigenomic and transcriptomic space.

Nature Methods, Research HighlightA new member of the spatial omics family.

Nature, Research BriefingsGene expression and epigenetic regulation co-mapped in brain tissues.

GenomewebNew Methods Enable Simultaneous Spatial Epigenome, Transcriptome Profiling.

Nature Structural & Molecular Biology, Research HighlightChromatin found in space.

GenomewebYale University, Karolisnka Institute Researchers Advance Spatial Chromatin Accessibility Profiling.

Nature Methods, Research HighlightMultiomics sequencing goes spatial.