Christine Cheng, PhD

Associate Professor
858-200-1864

Christine S. Cheng is an associate professor in the Informatics group at JCVI’s La Jolla Campus. After completing her doctoral research, Dr. Cheng did her postdoctoral training with Dr. Aviv Regev at the Broad Institute of MIT and Harvard. Dr. Cheng’s laboratory at JCVI includes both wet-lab (experimental) and dry-lab (computational) research. Dr. Cheng’s research program studies transcriptional regulatory networks and aims to develop a comprehensive understanding of how aberrant regulatory circuits contribute to human disease.

Dr. Cheng’s lab utilizes single cell droplet-based technology enabled by microfluidic device to simultaneously profile the transcriptome and epigenome of thousands of single cells at the same time. The main focus of her lab is to utilize single cell resolution functional genomic assays and computational methods to study heterogeneous clinical tissue samples and blood immune cell populations in patient samples.

Current projects focus on applying single-cell transcriptomics and epigenetics in Alzheimer’s disease and opioid use disorder patient samples, with the goal of finding diagnostic markers and therapeutic targets.

Dr. Cheng received her master’s degree in computer science from Stanford University and she received her doctorate degree in bioinformatics and systems biology from University of California, San Diego.

Related

Cirriculum Vitae (PDF)

Research Priorities

Understanding neuroinflammation in neurodegenerative diseases
  • Characterize dysregulated transcriptional regulatory circuitry in Alzheimer’s disease patients using single cell transcriptomics analysis
  • Develop novel 3D organoid-like spheroid model for Alzheimer’s disease
Understanding molecular changes in opioid use disorder
  • Characterize peripheral immune cell of opioid users using single cell transcriptomics
  • Utilize single cell transcriptomics to understand molecular changes in the brain of opioid use disorder patients

Publications

Karagiannis TT, Cleary JP, Gok B, Henderson AJ, Martin NG, Yajima M, Nelson EC, Cheng CS
Single cell transcriptomics reveals opioid usage evokes widespread suppression of antiviral gene program.
Nature communications. 2020-05-26; 11.1: 2611.
PMID: 32457298
Rickner HD, Niu SY, Cheng CS
ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes.
Journal of visualized experiments : JoVE. 2019-03-22; 145:
PMID: 30958473
Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang SC, Durand NC, Feng T, De Jager PL, Chang HY, Aiden EL, Benoist C, Beer MA, Ye CJ, Regev A
Genetic determinants of co-accessible chromatin regions in activated T cells across humans.
Nature genetics. 2018-08-01; 50.8: 1140-1150.
PMID: 29988122
Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai MM, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M
Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.
Cell. 2018-07-26; 174.3: 744-757.e24.
PMID: 29887377
Ji Z, He L, Rotem A, Janzer A, Cheng CS, Regev A, Struhl K
Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation.
Nature communications. 2018-05-25; 9.1: 2068.
PMID: 29802342
Soto-Feliciano YM, Bartlebaugh JME, Liu Y, Sánchez-Rivera FJ, Bhutkar A, Weintraub AS, Buenrostro JD, Cheng CS, Regev A, Jacks TE, Young RA, Hemann MT
PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes.
Genes & development. 2017-06-12; 31.10: 973-989.
PMID: 28607179
Fiziev P, Akdemir KC, Miller JP, Keung EZ, Samant NS, Sharma S, Natale CA, Terranova CJ, Maitituoheti M, Amin SB, Martinez-Ledesma E, Dhamdhere M, Axelrad JB, Shah A, Cheng CS, Mahadeshwar H, Seth S, Barton MC, Protopopov A, Tsai KY, Davies MA, Garcia BA, Amit I, Chin L, Ernst J, Rai K
Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression.
Cell reports. 2017-04-25; 19.4: 875-889.
PMID: 28445736
Cheng CS, Behar MS, Suryawanshi GW, Feldman KE, Spreafico R, Hoffmann A
Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms.
Cell systems. 2017-03-22; 4.3: 330-343.e5.
PMID: 28237795
Sanjana NE, Wright J, Zheng K, Shalem O, Fontanillas P, Joung J, Cheng C, Regev A, Zhang F
High-resolution interrogation of functional elements in the noncoding genome.
Science (New York, N.Y.). 2016-09-30; 353.6307: 1545-1549.
PMID: 27708104
Cheng CS, Rai K, Garber M, Hollinger A, Robbins D, Anderson S, Macbeth A, Tzou A, Carneiro MO, Raychowdhury R, Russ C, Hacohen N, Gershenwald JE, Lennon N, Nusbaum C, Chin L, Regev A, Amit I
Semiconductor-based DNA sequencing of histone modification states.
Nature communications. 2013-01-01; 4.2672.
PMID: 24157732
Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.
Molecular cell. 2012-09-14; 47.5: 810-22.
PMID: 22940246
Escoubet-Lozach L, Benner C, Kaikkonen MU, Lozach J, Heinz S, Spann NJ, Crotti A, Stender J, Ghisletti S, Reichart D, Cheng CS, Luna R, Ludka C, Sasik R, Garcia-Bassets I, Hoffmann A, Subramaniam S, Hardiman G, Rosenfeld MG, Glass CK
Mechanisms establishing TLR4-responsive activation states of inflammatory response genes.
PLoS genetics. 2011-12-08; 7.12: e1002401.
PMID: 22174696
Cheng CS, Feldman KE, Lee J, Verma S, Huang DB, Huynh K, Chang M, Ponomarenko JV, Sun SC, Benedict CA, Ghosh G, Hoffmann A
The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50.
Science signaling. 2011-02-22; 4.161: ra11.
PMID: 21343618
Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST
A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling.
Cell. 2009-07-10; 138.1: 114-28.
PMID: 19596239
Cheng CS, Johnson TL, Hoffmann A
Epigenetic control: slow and global, nimble and local.
Genes & development. 2008-05-01; 22.9: 1110-4.
PMID: 18451102
Kwon YS, Garcia-Bassets I, Hutt KR, Cheng CS, Jin M, Liu D, Benner C, Wang D, Ye Z, Bibikova M, Fan JB, Duan L, Glass CK, Rosenfeld MG, Fu XD
Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters.
Proceedings of the National Academy of Sciences of the United States of America. 2007-03-20; 104.12: 4852-7.
PMID: 17360330
Garcia-Bassets I, Kwon YS, Telese F, Prefontaine GG, Hutt KR, Cheng CS, Ju BG, Ohgi KA, Wang J, Escoubet-Lozach L, Rose DW, Glass CK, Fu XD, Rosenfeld MG
Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors.
Cell. 2007-02-09; 128.3: 505-518.
PMID: 17289570

Related

Cirriculum Vitae (PDF)

Research Priorities

Understanding neuroinflammation in neurodegenerative diseases
  • Characterize dysregulated transcriptional regulatory circuitry in Alzheimer’s disease patients using single cell transcriptomics analysis
  • Develop novel 3D organoid-like spheroid model for Alzheimer’s disease
Understanding molecular changes in opioid use disorder
  • Characterize peripheral immune cell of opioid users using single cell transcriptomics
  • Utilize single cell transcriptomics to understand molecular changes in the brain of opioid use disorder patients

Coronavirus Research

Overview of various projects related to the novel coronavirus pandemic.

Show Project