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 Subject Headings (MeSH)
- 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
Yuval Kluger, PhD
Anita Huttner, MD
Publications
2024
Spatially 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, 1-37. 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 investigationMLL1 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
Mapping RNA translation
Fan R. Mapping RNA translation. Science 2023, 380: 1321-1322. PMID: 37384700, DOI: 10.1126/science.adi6844.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMicrotechnologies for single-cell and spatial multi-omics
Deng Y, Bai Z, Fan R. Microtechnologies for single-cell and spatial multi-omics. Nature Reviews Bioengineering 2023, 1: 769-784. DOI: 10.1038/s44222-023-00084-y.Peer-Reviewed Original ResearchCitationsAltmetricConceptsSuch single-cell dataGene regulatory networksMulti-omics assaysSingle-cell dataMulti-omics studiesSingle cellsContext of tissuesGenome scaleRegulatory networksOmics informationGene expressionOmics assaysCellular profilingSubcellular levelIntact tissueCellsFunctional stateAssaysOmicsMicroarrayTissueProfilingRegulationExpressionMicrofluidic platformMicrofluidic Immuno‐Serolomic Assay Reveals Systems Level Association with COVID‐19 Pathology and Vaccine Protection
Kim D, Biancon G, Bai Z, VanOudenhove J, Liu Y, Kothari S, Gowda L, Kwan J, Buitrago‐Pocasangre N, Lele N, Asashima H, Racke M, Wilson J, Givens T, Tomayko M, Schulz W, Longbrake E, Hafler D, Halene S, Fan R. Microfluidic Immuno‐Serolomic Assay Reveals Systems Level Association with COVID‐19 Pathology and Vaccine Protection. Small Methods 2023, 7: e2300594. PMID: 37312418, PMCID: PMC10592458, DOI: 10.1002/smtd.202300594.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsB cell depletion therapyAcute COVID infectionAnti-spike IgGHigh-risk patientsCoronavirus disease-19COVID-19 pathologyDepletion therapyVaccine protectionAntibody responseCOVID infectionHematologic malignanciesImmune protectionDisease-19Healthy donorsMultiple time pointsSerology assaysBlood samplesSoluble markersB cellsImmunization strategiesPatientsFunctional deficiencySerological analysisTime pointsClonotype diversityThe technological landscape and applications of single-cell multi-omics
Baysoy A, Bai Z, Satija R, Fan R. The technological landscape and applications of single-cell multi-omics. Nature Reviews Molecular Cell Biology 2023, 24: 695-713. PMID: 37280296, PMCID: PMC10242609, DOI: 10.1038/s41580-023-00615-w.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsSingle-cell multi-omics technologiesMulti-omics technologiesMolecular cell biology researchCell lineage tracingCell biology researchBioinformatics toolsLineage tracingOmics methodsCell statesBiology researchMathematical modellingCancer geneticsOmics modalitiesComputational methodsEpitranscriptomeEpigenomeTranscriptomeGenomeProteomeOmicsOptimization of throughputGeneticsArt methodsTranslational researchUniquenessSecretory MPP3 reinforce myeloid differentiation trajectory and amplify myeloid cell production
Kang Y, Paik H, Zhang S, Chen J, Olson O, Mitchell C, Collins A, Swann J, Warr M, Fan R, Passegué E. Secretory MPP3 reinforce myeloid differentiation trajectory and amplify myeloid cell production. Journal Of Experimental Medicine 2023, 220: e20230088. PMID: 37115584, PMCID: PMC10140385, DOI: 10.1084/jem.20230088.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsGranulocyte/macrophage progenitorsHematopoietic stem cellsMyeloid differentiationMajor functional contributorsNovel regulatory functionLocal bone marrow (BM) microenvironmentSteady-state hematopoiesisDifferentiation trajectoriesRecent lineagesMyeloid cell productionCellular heterogeneityBone marrow microenvironmentRegulatory functionsFunctional contributorsMacrophage progenitorsSecretory cellsStem cellsMPP3Blood productionMarrow microenvironmentCell productionDifferentiationRapid productionDistinct subsetsMyelopoiesisSpecial Issue: Spatial Omics
Fan R, Bayraktar O. Special Issue: Spatial Omics. GEN Biotechnology 2023, 2: 61-62. DOI: 10.1089/genbio.2023.29076.cfp2.Peer-Reviewed Original Research
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