Rong Fan, PhD
Harold Hodgkinson Professor of Biomedical EngineeringCards
Appointments
Additional Titles
Professor, Pathology
Contact Info
Biomedical Engineering
55 Prospect St, MEC 213
New Haven, CT 06520
United States
Appointments
Additional Titles
Professor, Pathology
Contact Info
Biomedical Engineering
55 Prospect St, MEC 213
New Haven, CT 06520
United States
Appointments
Additional Titles
Professor, Pathology
Contact Info
Biomedical Engineering
55 Prospect St, MEC 213
New Haven, CT 06520
United States
About
Titles
Harold Hodgkinson Professor of Biomedical Engineering
Professor, Pathology
Biography
Dr. Rong Fan is the Harold Hodgkinson Professor of Biomedical Engineering and of Pathology. His research interest has been centered on the development and deployment of single-cell and spatial omics technologies to investigate normal development, aging, and disease. He received a B.S. in Applied Chemistry from University of Science and Technology of China, a Ph.D. in Chemistry from the University of California at Berkeley, and then completed his postdoctoral training at California Institute of Technology, prior to joining the faculty of Department of Biomedical Engineering at Yale University in 2010. He developed a microchip that allows for simultaneous measurement of 42 immune effector proteins in single cells at high throughput, which remains the highest multiplexing to date for a single-cell protein secretion assay. In collaboration with Novartis and Kite Pharma, it was applied to profiling antigen-specific activation states of chimeric antigen receptor (CAR)-engineered T cells, resulting in the discovery of novel single-cell biomarkers including polyfunctional strength index to characterize the quality of CAR-T infusion products and predict the clinical responses and immune-related adverse effects(irAEs) prior to treatment. This microchip, called IsoCode, and the automation system, called IsoLight, have been commercialized by IsoPlexis, a company co-founded by Dr. Fan. Now, this system has been used by >100 major pharmaceutical companies and cancer centers around the world for monitoring CAR-T or checkpoint inhibitor immunotherapies. Dr. Fan is also a pioneer in developing NGS-based spatial omics sequencing technologies. He conceived the concept of spatial multi-omics and developed the first spatially resolved multi-omics sequencing technology called DBiT-seq (Liu et al., Cell 183, 1665–1681, 2020) which allows for spatial co-profiling of whole transcriptome and hundreds of proteins (spatial-CITE-seq) at cellular level in complex tissues. He further developed a first-of-its-kind technology to enable spatial epigenome sequencing including spatial-ATAC-seq (Deng et al., Nature 609 (7926), 375-383, 2022) and spatial-CUT&Tag (Deng et al., Science 375 (6581), 681-686, 2022). These technologies may unlock a whole new field in spatial biology with applications in a wide range of biological and biomedical research. Dr. Fan co-founded IsoPlexis, Singleron Biotechnologies, and AtlasXomics. He is the recipient of multiple awards including the NCI Howard Temin Career Transition Award, the NSF CAREER Award, and the Packard Fellowship for Science and Engineering. He has been elected to American Institute for Medical and Biological Engineering (AIMBE), Connecticut Academy of Science and Engineering (CASE), and the National Academy of Inventors (NAI).
Appointments
Pathology
ProfessorSecondary
Other Departments & Organizations
- Cancer Signaling Networks
- Center for RNA Science and Medicine
- Computational Biology and Biomedical Informatics
- Dean's Workshops
- Global Health Studies
- Human and Translational Immunology Program
- Lu Lab
- Pathology
- Yale Cancer Center
- Yale Center for Research on Aging (Y-Age)
- Yale Combined Program in the Biological and Biomedical Sciences (BBS)
- Yale Stem Cell Center
- Yale Ventures
Education & Training
- PhD
- University of California, Berkeley (2006)
- BS
- University of Science and Technology of China (1999)
Research
Overview
BioMEMS; Single-Cell Omics: Spatial Omics; Hematology Oncology; Immunology
Medical Research Interests
- View Lab Website
Fan Lab
Research at a Glance
Yale Co-Authors
Publications Timeline
Research Interests
Joseph Craft, MD
Stephanie Halene, MD, Dr Med
David A. Hafler, MD, FANA
Mary Tomayko, MD, PhD
Mina Xu, MD
Yuval Kluger, PhD
Publications
2024
Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues
Bai Z, Zhang D, Gao Y, Tao B, Zhang D, Bao S, Enninful A, Wang Y, Li H, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu M, Fan R. Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues. Cell 2024, 187: 6760-6779.e24. PMID: 39353436, DOI: 10.1016/j.cell.2024.09.001.Peer-Reviewed Original ResearchConceptsRNA biologyWhole-transcriptome sequencingMicroRNA regulatory networkSplicing dynamicsDeterministic barcodingRNA speciesRNA processingRNA variantsFFPE tissuesRegulatory networksTranscriptome sequencingSpliced isoformsNon-malignant cellsTumor clonal architecturesClonal architectureGene expressionCellular dynamicsRNAArchival formalin-fixed paraffin-embedded tissueMalignant subclonesFormalin-fixed paraffin-embedded (FFPEFFPE samplesParaffin-embedded (FFPEBiologyHuman lymphomasThe type 2 cytokine Fc–IL-4 revitalizes exhausted CD8+ T cells against cancer
Feng B, Bai Z, Zhou X, Zhao Y, Xie Y, Huang X, Liu Y, Enbar T, Li R, Wang Y, Gao M, Bonati L, Peng M, Li W, Tao B, Charmoy M, Held W, Melenhorst J, Fan R, Guo Y, Tang L. The type 2 cytokine Fc–IL-4 revitalizes exhausted CD8+ T cells against cancer. Nature 2024, 634: 712-720. PMID: 39322665, PMCID: PMC11485240, DOI: 10.1038/s41586-024-07962-4.Peer-Reviewed Original ResearchAltmetricConceptsCD8+ T cellsMammalian target of rapamycinCancer immunotherapyT cellsNext-generation cancer immunotherapyAdoptive T-cell transferImmune checkpoint blockade therapyLong-term complete remissionCurrent cancer immunotherapiesCheckpoint blockade therapyInduce durable remissionsT-cell transferCD8+ TCytokine-based immunotherapyType 2 cytokinesXenograft tumor modelBlockade therapyDurable remissionsComplete remissionAntitumour efficacyTumor modelTarget of rapamycinInterleukin-4Immune responseCD8Single-cell CAR T atlas reveals type 2 function in 8-year leukaemia remission
Bai Z, Feng B, McClory S, de Oliveira B, Diorio C, Gregoire C, Tao B, Yang L, Zhao Z, Peng L, Sferruzza G, Zhou L, Zhou X, Kerr J, Baysoy A, Su G, Yang M, Camara P, Chen S, Tang L, June C, Melenhorst J, Grupp S, Fan R. Single-cell CAR T atlas reveals type 2 function in 8-year leukaemia remission. Nature 2024, 634: 702-711. PMID: 39322664, PMCID: PMC11485231, DOI: 10.1038/s41586-024-07762-w.Peer-Reviewed Original ResearchAltmetricConceptsChimeric antigen receptorChimeric antigen receptor T cellsT cellsIL-4CAR T-cell dysfunctionChimeric antigen receptor T-cell productsCAR-T cell persistenceProteomic profiling of seraCAR-T cellsT cell persistenceT-cell therapyLong-term remissionT cell dysfunctionCAR-T productsType 2 cytokinesAntigen-specific activationT cell productionAssociated with patientsType 2 cellsDysfunctional subsetPotential therapeutic strategyCellular immunotherapyLeukemia remissionPatients relapseType 2 functionsSpatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue
Farzad N, Enninful A, Bao S, Zhang D, Deng Y, Fan R. Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue. Nature Protocols 2024, 19: 3389-3425. PMID: 38943021, DOI: 10.1038/s41596-024-01013-y.Peer-Reviewed Original ResearchCitationsAltmetricConceptsTn5 transpositionDeterministic barcodingGenome-wide profiling of histone modificationsProfiling of histone modificationsTransposase-accessible chromatin sequencingEpigenomic profiling methodsGenome-wide profilingSingle-base resolutionGene regulation programsGenomic DNA locusNext-generation sequencingDNA lociBioinformatics skillsLibrary preparationDNA barcodingChromatin accessibilityChromatin sequencingHistone modificationsEpigenome sequencingEpigenetic landscapeEpigenetic mapsCellular functionsEpigenetic markersCustom pipelineBarcodingSenNet recommendations for detecting senescent cells in different tissues
Suryadevara V, Hudgins A, Rajesh A, Pappalardo A, Karpova A, Dey A, Hertzel A, Agudelo A, Rocha A, Soygur B, Schilling B, Carver C, Aguayo-Mazzucato C, Baker D, Bernlohr D, Jurk D, Mangarova D, Quardokus E, Enninga E, Schmidt E, Chen F, Duncan F, Cambuli F, Kaur G, Kuchel G, Lee G, Daldrup-Link H, Martini H, Phatnani H, Al-Naggar I, Rahman I, Nie J, Passos J, Silverstein J, Campisi J, Wang J, Iwasaki K, Barbosa K, Metis K, Nernekli K, Niedernhofer L, Ding L, Wang L, Adams L, Ruiyang L, Doolittle M, Teneche M, Schafer M, Xu M, Hajipour M, Boroumand M, Basisty N, Sloan N, Slavov N, Kuksenko O, Robson P, Gomez P, Vasilikos P, Adams P, Carapeto P, Zhu Q, Ramasamy R, Perez-Lorenzo R, Fan R, Dong R, Montgomery R, Shaikh S, Vickovic S, Yin S, Kang S, Suvakov S, Khosla S, Garovic V, Menon V, Xu Y, Song Y, Suh Y, Dou Z, Neretti N. SenNet recommendations for detecting senescent cells in different tissues. Nature Reviews Molecular Cell Biology 2024, 1-23. PMID: 38831121, DOI: 10.1038/s41580-024-00738-8.Peer-Reviewed Original ResearchCitationsAltmetricConceptsSenescent cellsDetect senescent cellsIrreversible cell cycle arrestCellular senescenceCell cycle arrestSenescence markersBiomarker Working GroupCycle arrestCellular senescence markersBiological processesCell biologyPostmitotic cellsSenescent phenotypeCirculating markersTissue culture studiesSenescence signatureSenescenceCellsMorphological featuresDetrimental roleTissueMarkersSeasonal investigationMulti-Omics Profiling of Human Hippocampus Reveals Increased Inflammation and Transcription Instability in Major Depressive Disorder
Xiao Y, Mariani M, Su G, Deng Y, Sissoko C, Li T, Ma S, Bai Z, Liu Y, Rosoklija G, Wu T, Dwork A, Hen R, Mann J, Fan R, Leong K, Boldrini M. Multi-Omics Profiling of Human Hippocampus Reveals Increased Inflammation and Transcription Instability in Major Depressive Disorder. Biological Psychiatry 2024, 95: s68-s69. DOI: 10.1016/j.biopsych.2024.02.168.Peer-Reviewed Original ResearchMLL1 regulates cytokine-driven cell migration and metastasis
Nair P, Danilova L, Gómez-de-Mariscal E, Kim D, Fan R, Muñoz-Barrutia A, Fertig E, Wirtz D. MLL1 regulates cytokine-driven cell migration and metastasis. Science Advances 2024, 10: eadk0785. PMID: 38478601, PMCID: PMC10936879, DOI: 10.1126/sciadv.adk0785.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsMethyltransferase mixed-lineage leukemia 1Cell migrationControls actin filament assemblyRegulation of cell migrationHistone methyltransferase mixed-lineage leukemia 1Actin filament assemblyCell cycle-related pathwaysCancer cell migrationMixed-lineage leukemia 1Regulating cell proliferationMyosin contractilityFilament assemblyProtein meninAssociated with immune cellsMetastatic burdenCancer cellsCell proliferationPrimary tumor growth rateLung metastatic burdenTumor growth rateGrowth rateCellsPreexisting metastasesMetastatic diseaseTumor growthAuthor Correction: Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments
Janiszewska M, Tabassum D, Castaño Z, Cristea S, Yamamoto K, Kingston N, Murphy K, Shu S, Harper N, Del Alcazar C, Alečković M, Ekram M, Cohen O, Kwak M, Qin Y, Laszewski T, Luoma A, Marusyk A, Wucherpfennig K, Wagle N, Fan R, Michor F, McAllister S, Polyak K. Author Correction: Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments. Nature Cell Biology 2024, 26: 841-841. PMID: 38443568, DOI: 10.1038/s41556-024-01385-z.Peer-Reviewed Original ResearchConcepts
2023
229 Large-scale omics profiling reveals type-2 functionality sustaining 8-year leukemia remission following CAR T cell therapy
Bai Z, Feng B, McClory S, Diorio C, Zhao Z, Tang L, Melenhorst J, June C, Grupp S, Fan R. 229 Large-scale omics profiling reveals type-2 functionality sustaining 8-year leukemia remission following CAR T cell therapy. 2023, a261-a264. DOI: 10.1136/jitc-2023-sitc2023.0229.Peer-Reviewed Original ResearchSingle-Cell Multi-Omics Reveals Type-2 Functionality in Maintaining CAR T Cell Longevity Associated with 8-Year Leukemia Remission
Bai Z, Feng B, Mcclory S, Diorio C, Zhao Z, Tang L, Melenhorst J, June C, Grupp S, Fan R. Single-Cell Multi-Omics Reveals Type-2 Functionality in Maintaining CAR T Cell Longevity Associated with 8-Year Leukemia Remission. Blood 2023, 142: 352. DOI: 10.1182/blood-2023-179480.Peer-Reviewed Original ResearchCitationsConceptsChimeric antigen receptor T cellsCAR-T cellsChimeric antigen receptorType 2 cytokinesB-cell aplasiaT cellsAcute lymphocytic leukemiaCAR-T persistenceIL-4CAR-TType 1Validation cohortCAR T infusionSurvival of tumor-bearing miceDiscovery cohortPersistent CAR T cellsDose of tumor cellsLevels of type 2 cytokinesType 2 cytokine levelsNSG mouse modelPediatric ALL patientsLong-term remissionReduced tumor burdenT cell longevityType 1 cytokines
News
News
- September 30, 2024
New Barcode Technology Could Help Diagnose Cancer More Precisely
- September 25, 2024Source: Yale Engineering
Study reveals possible key to long-term survival among CAR T therapy patients
- September 05, 2024
Five Yale Investigators Receive NIH U01 Award
- March 15, 2023Source: Yale Biomedical Engineering
New Technology Simultaneously Maps Gene Activity and Expression
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Biomedical Engineering
55 Prospect St, MEC 213
New Haven, CT 06520
United States