Rong Fan

Rong Fan

Website:

Fan Lab
Harold Hodgkinson Professor of Biomedical Engineering and Pathology
Room / Office: Malone 213
Office Address:
55 Prospect Street
New Haven, CT 06511
Mailing Address:
P.O. Box 208260
New Haven, CT 06520
Phone: (203) 432-9905
Email: rong.fan@yale.edu
Degrees:
  • Ph.D., University of California, Berkeley
  • B.S., University of Science and Technology of China

Interests:

Dr. Rong Fan is the Harold Hodgkinson Professor of Biomedical Engineering and of Pathology. His research interest has been centered on development and deployment of single-cell and spatial omics technologies for the study of human tissue function in normal physiology, aging, and disease. He developed single-cell 42-plex cytokine assay which remains the highest multiplex for single-cell protein secretion measurement. He conceived and demonstrated the first "spatial multi-omics" sequencing by developing a unique approach named deterministic barcoding in tissue (DBiT) for mapping whole transcriptome and ~300 proteins pixel-by-pixel directly on a fixed tissue section. His research also led to the debut of a new dimension in spatial omics – "spatial epigenomics" – with the development of spatial-ATAC-seq, spatial-CUT&Tag, and spatial epigenome-transcriptome co-profiling. Recently, he further developed Patho-DBiT for pathology-compatible spatial profiling of all kinds of RNA species including mRNA, splicing isoforms, microRNA, tRNA, snoRNA, snRNA, and even single nucleotide variants and RNA editing in archival FFPE tissue specimens. These technologies have been applied to the study of human and mouse brain development, neuroinflammation, cellular senescence and aging, tumor initiation, progression and metastasis, and human cardiovascular diseases. Spatial multi-omics is poised to fuel the next wave of biomedical research revolution and facilitate clinical biomarker discovery and therapeutic development.

Selected Awards & Honors:

  • The Momentum Award, CMBE, Biomedical Engineering Society (BMES) (2024)
  • Benjamin Highman Endowed Lectureship, UC Davis Medical Center (2023)
  • Class 1961 Cancer Research Award (2022)
  • Fellow, the National Academy of Inventors (NAI) (2021)
  • Yale Cancer Center Class of 1961 Cancer Research Award (2021)
  • Member, Connecticut Academy of Science and Engineering (2021)
  • Fellow, the American Institute for Medical and Biological Engineering (AIMBE) (2019)
  • Stand Up to Cancer (SU2C), the Functional CART Cell Convergence Team Award (team lead) (2018)
  • The Rising Star Award, Cellular and Molecular Bioengineering (CMBE) SIG, BMES (2016)
  • Kavli Fellow - Invited to attend 2014 US Kavli Frontier in Science Symposium, National Academy of Sciences (2014)
  • Emerging Investigator – Lab on a Chip Special Issue (2014)
  • National Science Foundation, the Faculty Early Career Development (CAREER) Award (2014)
  • Packard Fellowship for Science and Engineering (2012)
  • Alzheimer's Association, New Investigator Research Award (2010)
  • Bill & Melinda Gates Foundation, Grand Challenges Exploration Award (2010)
  • National Cancer Institute, Howard Temin Pathway to Independence (K99/R00) Award (2009-2013)

Selected Publications:

  • Zhiliang Bai, Dingyao Zhang, Yan Gao, Bo Tao, Shuozhen Bao, Archibald Enninful, Daiwei Zhang, Graham Su, Xiaolong Tian, Ningning Zhang, Yang Liu, Mark Gerstein, Mingyao Li*, Yi Xing*, Jun Lu*, Mina Xu*, & Rong Fan*, Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues via Patho-DBiT, Cell 187, 6760–6779 (2024). (Cover Highlight) [LINK]
  • Zhiliang Bai, Bing Feng, Susan E. McClory, Beatriz Coutinho de Oliveira, Caroline Diorio, Céline Gregoire, Bo Tao, Luojia Yang, Ziran Zhao, Lei Peng, Giacomo Sferruzza, Liqun Zhou, Xiaolei Zhou, Jessica Kerr, Alev Baysoy, Graham Su, Mingyu Yang, Pablo G. Camara, Sidi Chen, Li Tang, Carl H. June, J. Joseph Melenhorst, Stephan A. Grupp, and Rong Fan*. Single-cell CAR T atlas reveals type-2 function in 8-year leukemia remission, Nature, 634, 702–711 (2024).  [LINK]
  • Di Zhang, Yanxiang Deng, Petra Kukanja, Eneritz Agirre, Marek Bartosovic, Mingze Dong, Cong Ma, Sai Ma, Graham Su, Shuozhen Bao, Yang Liu, Yang Xiao, Gorazd B. Rosoklija, Andrew J. Dwork, J. John Mann, Kam W. Leong, Maura Boldrini, Liya Wang, Maximilian Haeussler, Benjamin J. Raphael, Yuval Kluger, Gonçalo Castelo-Branco, Rong Fan*, Spatial epigenome-transcriptome co-profiling of mammalian tissues, Nature, 616, 113–122 (2023) [LINK]
  • Yang Liu, Marcello DiStasio, Graham Su, Hiromitsu Asashima, Archibald Enninful, Xiaoyu Qin, Yanxiang Deng, Pino Bordignon, Marco Cassano, Mary Tomayko, Mina Xu, Stephanie Halene, Joseph E. Craft, David Hafler, and Rong Fan*, High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq, Nature Biotechnology, 41, 1405–1409 (2023). [LINK]
  • Yanxiang Deng, Marek Bartosovic, Sai Ma, Di Zhang, Petra Kukanja, Yang Xiao, Graham Su, Yang Liu, Xiaoyu Qin, Gorazd B Rosoklija, Andrew J Dwork, J John Mann, Mina L Xu, Stephanie Halene, Joseph E Craft, Kam W Leong, Maura Boldrini, Gonçalo Castelo-Branco*, Rong Fan*. Spatial profiling of chromatin accessibility in mouse and human tissues. Nature, 609, 375–383 (2022). [LINK]
  • Yanxiang Deng, Marek Bartosovic, Petra Kukanja, Di Zhang, Yang Liu, Graham Su, Archibald Enninful, Zhiliang Bai, Gonçalo Castelo-Branco, Rong Fan*. Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. Science, 375(6581):681-686 (2022). [LINK]
  • Yang Liu, Mingyu Yang, Yanxiang Deng, Graham Su, Archibald Enninful, Cindy C. Guo, Toma Tebaldi, Di Zhang, Dongjoo Kim, Zhiliang Bai, Eileen Norris, Alisia Pan, Jiatong Li, Yang Xiao, Stephanie Halene, and Rong Fan*, High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue, Cell, 183, 1665-1681 (2020). [LINK]
  • Wang N, Zheng J, Chen Z, Liu Y, Dura B, Kwak M, Xavier-Ferrucio J, Lu Y-C,Zhang MM, Roden C, Cheng JJ, Krause D, Ding Y, Fan R* & Lu J*. Single-cell microRNA/mRNA co-profiling reveals non-(epigenetic) heterogeneity and regulatory programs. Nature Communications, 10: 95 (2019). [LINK]
  • Xhangolli I, Dura B, Lee GH, Kim DJ, Xiao Y, and Fan R*. Single-cell integrative analysis of CAR-T cell activation reveals a predominantly TH1/TH2 mixed response independent of differentiation, Genomics, Proteomics & Bioinformatics (GPB), 17(2), 129-139 (2019). (Cover Highlight) [LINK]
  • Xiao Y, Kim DJ, Dura B, Zhang K, Yan RC, Li HM, Han E, Ip J, Zou P, Liu J, Chen AT, Vortmeyer AO, Zhou JB, and Fan R*, Ex vivo dynamics of human glioblastoma cells in a microvasculature-on-a-chip system correlates with tumor heterogeneity and subtypes, Advanced Science, 6, 1801531 (2019). (Cover Highlight) [LINK]
  • Dura B, Choi JY, Zhang K, Damsky W, Thakral D, Bosenberg M, Craft J, Fan R*, scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3’ mRNA profiling, Nucleic Acids Research, 47(3), e16 (2019). [LINK]
  • Kleppe M, Kwak M, Koppikar P, Riester M, Keller M, Bastian L, Hricik T, Bhagwat N, Abdel-Wahab OI, Marubayashi S, Chen JJ, Romanet V, Fridman JS, Bromberg J, Murakami M, Radimerski T, Michor F, Fan R* & Levine RL*.  JAK-STAT Pathway Activation in Malignant and Non-Malignant Cells Contributes to MPN Pathogenesis and Therapeutic Response, Cancer Discovery, 5(3), 316–31 (2015). [LINK]
  • Xue Q, Lu Y, Eisele MR, Sulistijo E, Fan R* & Miller-Jensen K*, Analysis of single-cell secretion reveals a role for paracrine signaling in coordinating macrophage response to TLR4 stimulation, Science Signaling, 8, 381 (2015). [LINK]
  • Lu Y, Xue Q, Eisele MR, Sulistijo E, Brower K, Han L, Amir ED, Pe’er D, Miller-Jensen K *, and Fan R*,  Highly multiplexed profiling of immune effector functions reveals deep functional heterogeneity in response to pathogenic ligands, Proc. Natl. Acad. Sci., U.S.A., 112(7), 607-615 (2015). [LINK]