Jeffrey Cheng, MD, PhD
Associate Professor
Dermatology
School of Medicine

Education & Training

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• M.D. School of Medicine University of Texas Southwestern 2006

Websites

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• The RashX Project at UCSF (rashx.ucsf.edu)

Grants and Projects

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• Precision medicine approaches to chronic inflammatory skin disease of older veterans, Veterans Health Administration, 2023-2027
• Single Cell Transcriptomic Classification of Inflammatory Skin Disease, LEO Foundation, 2022-2025
• Spatial Analysis of Alopecia Areata Inflammation, Pfizer Global Medical Grants, 2021-2023
• Role of DNA Methylation and Hydroxymethylation in Epidermal Homeostasis, NIH, 2015-2021

Publications (38)

Top publication keywords:
PsoriasisSkin Physiological PhenomenaSingle-Cell AnalysisWaxesEpidermisSteroid HydroxylasesGenome, HumanExanthemaSkin DiseasesDermatitis, AtopicSkin NeoplasmsTranscription, Genetic25-Hydroxyvitamin D3 1-alpha-HydroxylaseEctodermEpigenesis, Genetic

• A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity.
  Cell reports. Medicine 2022 Cook CP, Taylor M, Liu Y, Schmidt R, Sedgewick A, Kim E, Hailer A, North JP, Harirchian P, Wang H, Kashem SW, Shou Y, McCalmont TC, Benz SC, Choi J, Purdom E, Marson A, Ramos SBV, Cheng JB, Cho RJ
• Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution.
  Cell reports 2018 Cheng JB, Sedgewick AJ, Finnegan AI, Harirchian P, Lee J, Kwon S, Fassett MS, Golovato J, Gray M, Ghadially R, Liao W, Perez White BE, Mauro TM, Mully T, Kim EA, Sbitany H, Neuhaus IM, Grekin RC, Yu …
• Preexisting Skin-Resident CD8 and γδ T-cell Circuits Mediate Immune Response in Merkel Cell Carcinoma and Predict Immunotherapy Efficacy.
  Cancer discovery 2024 Reinstein ZZ, Zhang Y, Ospina OE, Nichols MD, Chu VA, Pulido AM, Prieto K, Nguyen JV, Yin R, Moran Segura C, Usman A, Sell B, Ng S, de la Iglesia JV, Chandra S, Sosman JA, Cho RJ, Cheng JB, Ivanova E,…
• Discovery and generalization of tissue structures from spatial omics data.
  Cell reports methods 2024 Wu Z, Kondo A, McGrady M, Baker EAG, Chidester B, Wu E, Rahim MK, Bracey NA, Charu V, Cho RJ, Cheng JB, Afkarian M, Zou J, Mayer AT, Trevino AE
• Short cell cycle duration is a phenotype of human epidermal stem cells.
  Stem cell research & therapy 2024 Xiao T, Eze UC, Charruyer-Reinwald A, Weisenberger T, Khalifa A, Abegaze B, Schwab GK, Elsabagh RH, Parenteau TR, Kochanowski K, Piper M, Xia Y, Cheng JB, Cho RJ, Ghadially R

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• A single-cell atlas of IL-23 inhibition in cutaneous psoriasis distinguishes clinical response.
  Science immunology 2024 Wu D, Hailer AA, Wang S, Yuan M, Chan J, El Kurdi A, Rahim M, Kondo A, Han D, Ali H, D'Angio B, Mayer A, Klufas D, Kim E, Shain AH, Choi J, Bhutani T, Simpson G, Grekin RC, Ricardo-Gonzalez R, Purdom …
• STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer.
  Genome biology 2023 Chen L, Chang D, Tandukar B, Deivendran D, Pozniak J, Cruz-Pacheco N, Cho RJ, Cheng J, Yeh I, Marine C, Bastian BC, Ji AL, Shain AH
• GLUT3 promotes macrophage signaling and function via RAS-mediated endocytosis in atopic dermatitis and wound healing.
  The Journal of clinical investigation 2023 Yu DM, Zhao J, Lee EE, Kim D, Mahapatra R, Rose EK, Zhou Z, Hosler C, El Kurdi A, Choe JY, Abel ED, Hoxhaj G, Westover KD, Cho RJ, Cheng JB, Wang RC
• Optimizing Single T-Cell Transcriptomic Discrimination of Atopic Dermatitis Versus Psoriasis Vulgaris.
  The Journal of investigative dermatology 2023 Taylor MA, El Kurdi A, Hailer A, Wang S, Yuan M, Mukhopadhyay S, Bhutani T, North JP, Cho RJ, Cheng JB
• Isolation of human cutaneous immune cells for single-cell RNA sequencing.
  STAR protocols 2023 Hailer AA, Wu D, El Kurdi A, Yuan M, Cho RJ, Cheng JB
• Transcriptomics aids differentiation of IL-23 overactivity in a patient with atypical skin and joint disease.
  Lancet (London, England) 2023 Hakimi M, North JP, Taylor MA, Hailer A, Liu Y, Kim E, Morehead K, Shinkai K, Bhutani T, Cheng JB, Cho RJ
• A Novel Potential Role for Monocytes Revealed by Single Cell Analysis of Immunotherapy Induced Immune Related Adverse Events.
  Cancers 2022 Garrison Z, Chang M, Hornick N, Yu WY, Cheng JB, Kulkarni RP
• Circulating biomarkers of response to immunotherapy and immune-related adverse events.
  Expert review of molecular diagnostics 2022 Garrison Z, Hornick N, Cheng J, Kulkarni RP
• Defining Patient-Level Molecular Heterogeneity in Psoriasis Vulgaris Based on Single-Cell Transcriptomics.
  Frontiers in immunology 2022 Liu Y, Wang H, Cook C, Taylor MA, North JP, Hailer A, Shou Y, Sadik A, Kim E, Purdom E, Cheng JB, Cho RJ
• Spectral clustering of single-cell multi-omics data on multilayer graphs.
  Bioinformatics (Oxford, England) 2022 Zhang S, Leistico JR, Cho RJ, Cheng JB, Song JS
• Classification of human chronic inflammatory skin disease based on single-cell immune profiling.
  Science immunology 2022 Liu Y, Wang H, Taylor M, Cook C, Martínez-Berdeja A, North JP, Harirchian P, Hailer AA, Zhao Z, Ghadially R, Ricardo-Gonzalez RR, Grekin RC, Mauro TM, Kim E, Choi J, Purdom E, Cho RJ, Cheng JB
• Single-Cell Profiling Reveals Divergent, Globally Patterned Immune Responses in Murine Skin Inflammation.
  iScience 2020 Liu Y, Cook C, Sedgewick AJ, Zhang S, Fassett MS, Ricardo-Gonzalez RR, Harirchian P, Kashem SW, Hanakawa S, Leistico JR, North JP, Taylor MA, Zhang W, Man MQ, Charruyer A, Beliakova-Bethell N, Benz SC…
• Riemannian geometry and statistical modeling correct for batch effects and control false discoveries in single-cell surface protein count data.
  Physical review. E 2020 Zhang S, Leistico JR, Cook C, Liu Y, Cho RJ, Cheng JB, Song JS
• Single-Cell Transcriptomics Reveals Spatial and Temporal Turnover of Keratinocyte Differentiation Regulators.
  Frontiers in genetics 2019 Finnegan A, Cho RJ, Luu A, Harirchian P, Lee J, Cheng JB, Song JS
• A20 and ABIN1 Suppression of a Keratinocyte Inflammatory Program with a Shared Single-Cell Expression Signature in Diverse Human Rashes
  J Invest Dermatol 2019 Harirchian P, Lee J, Hilz S, Sedgewick AJ, Perez White BE, Kesling MJ, Mully T, Golovato J, Gray M, Mauro TM, Purdom E, Kim EA, Sbitany H, Bhutani T, Vaske CJ, Benz SC, Cho RJ, Cheng JB
• Local genomic features predict the distinct and overlapping binding patterns of the bHLH-Zip family oncoproteins MITF and MYC-MAX.
  Pigment cell & melanoma research 2018 Hejna M, Moon WM, Cheng J, Kawakami A, Fisher DE, Song JS
• Emergence and Evolution of Mutational Hotspots in Sun-Damaged Skin.
  The Journal of investigative dermatology 2018 Cheng JB, Cho RJ
• Induced Pluripotent Stem Cell Differentiation and Three-Dimensional Tissue Formation Attenuate Clonal Epigenetic Differences in Trichohyalin.
  Stem cells and development 2016 Petrova A, Capalbo A, Jacquet L, Hazelwood-Smith S, Dafou D, Hobbs C, Arno M, Farcomeni A, Devito L, Badraiq H, Simpson M, McGrath JA, Di WL, Cheng JB, Mauro TM, Ilic D
• Integrative analysis of 111 reference human epigenomes.
  Nature 2015 Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon …
• Epigenetic and transcriptional determinants of the human breast.
  Nature communications 2015 Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, …
• Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.
  Nature communications 2014 Lowdon RF, Zhang B, Bilenky M, Mauro T, Li D, Gascard P, Sigaroudinia M, Farnham PJ, Bastian BC, Tlsty TD, Marra MA, Hirst M, Costello JF, Wang T, Cheng JB
• Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes.
  Cell reports 2014 Zheng CL, Wang NJ, Chung J, Moslehi H, Sanborn JZ, Hur JS, Collisson EA, Vemula SS, Naujokas A, Chiotti KE, Cheng JB, Fassihi H, Blumberg AJ, Bailey CV, Fudem GM, Mihm FG, Cunningham BB, Neuhaus IM, …
• ALEA: a toolbox for allele-specific epigenomics analysis.
  Bioinformatics (Oxford, England) 2013 Younesy H, Möller T, Heravi-Moussavi A, Cheng JB, Costello JF, Lorincz MC, Karimi MM, Jones SJ
• Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.
  Cell 2013 Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R, Haugen E, Heimfeld S, Murry CE, Akey JM, Stamatoyannopoulos JA
• Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.
  Genome research 2013 Stevens M, Cheng JB, Li D, Xie M, Hong C, Maire CL, Ligon KL, Hirst M, Marra MA, Costello JF, Wang T
• Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm.
  Genome research 2013 Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, Cheng JB, Li D, Stevens M, Lee HJ, Xing X, Zhou J, Sundaram V, Elliott G, Gu J, Shi T, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A…
• Genetics and epigenetics of the skin meet deep sequence.
  The Journal of investigative dermatology 2012 Cheng JB, Cho RJ
• Mammalian wax biosynthesis. I. Identification of two fatty acyl-Coenzyme A reductases with different substrate specificities and tissue distributions.
  The Journal of biological chemistry 2004 Cheng JB, Russell DW
• Mammalian wax biosynthesis. II. Expression cloning of wax synthase cDNAs encoding a member of the acyltransferase enzyme family.
  The Journal of biological chemistry 2004 Cheng JB, Russell DW
• Genetic evidence that the human CYP2R1 enzyme is a key vitamin D 25-hydroxylase.
  Proceedings of the National Academy of Sciences of the United States of America 2004 Cheng JB, Levine MA, Bell NH, Mangelsdorf DJ, Russell DW
• De-orphanization of cytochrome P450 2R1: a microsomal vitamin D 25-hydroxilase.
  The Journal of biological chemistry 2003 Cheng JB, Motola DL, Mangelsdorf DJ, Russell DW
• Molecular genetics of 3beta-hydroxy-Delta5-C27-steroid oxidoreductase deficiency in 16 patients with loss of bile acid synthesis and liver disease.
  The Journal of clinical endocrinology and metabolism 2003 Cheng JB, Jacquemin E, Gerhardt M, Nazer H, Cresteil D, Heubi JE, Setchell KD, Russell DW
• A box H/ACA small nucleolar RNA-like domain at the human telomerase RNA 3' end.
  Molecular and cellular biology 1999 Mitchell JR, Cheng J, Collins K