Micah Luftig

Overview:

The laboratory focuses on the mechanisms by which Epstein-Barr virus activates and ultimately subverts the host oncogenic stress response to growth transform primary B lymphocytes into indefinitely proliferating lymphoblastoid cell lines (LCLs). EBV infection of B cells leads to a latent growth program where eight viral proteins and several non-coding RNAs are expressed. Among these gene products, latent membrane protein 1 (LMP1) and Epstein-Barr virus nuclear antigen (EBNA) 2 are the core transforming oncogenes. These proteins are capable of driving B cell proliferation and act to suppress the apoptotic response induced by aberrant S phase induction. The goals of the laboratory include: i) understanding the host pathways that respond to and suppress EBV-mediated growth transformation, ii) understanding the viral gene products important for activating the oncogenic stress response and ultimately overcoming this response, and iii) identifying and characterizing a cell population within the CD21-expressing primary B cell population that has an increased susceptibility to oncogenic stress.

The biochemical and genetic analyses of these pathways will provide valuable insight into our understanding of oncogenes and oncogenic viruses and the host cell response to such insults. Further, detailed understanding of the virus/host interaction may allow for the identification of specific pathways for therapeutic intervention in EBV-associated malignancies and possibly more broadly in malignancies which rely on similar pathways for their proliferation, survival, or self-renewal.

Positions:

Associate Professor of Molecular Genetics and Microbiology

Molecular Genetics and Microbiology
School of Medicine

Vice-Chair in the Department of Molecular Genetics and Microbiology

Molecular Genetics and Microbiology
School of Medicine

Associate Professor of Medicine

Medicine, Hematologic Malignancies and Cellular Therapy
School of Medicine

Associate Professor of Immunology

Immunology
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

Ph.D. 2003

Harvard University

Grants:

NIAID Virology Quality Assurance - Base to Opt 6

Administered By
Duke Human Vaccine Institute
Awarded By
National Institutes of Health
Role
Co Investigator
Start Date
End Date

Novel regulatory controls of Hepatitis C Virus envelopment and secretion by the viral NS4A protein

Administered By
Molecular Genetics and Microbiology
Awarded By
National Institutes of Health
Role
Co-Sponsor
Start Date
End Date

Host pathways regulating Epstein-Barr virus-mediated B cell growth transformation

Administered By
Molecular Genetics and Microbiology
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Targeting Apoptosis and Immune Control of Epstein-Barr Virus Infected Tonsillar B Cells

Administered By
Molecular Genetics and Microbiology
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

The role of EBNA3A in the survival of Epstein-Barr Virus-infected tonsillar B cells

Administered By
Molecular Genetics and Microbiology
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Publications:

Epstein-Barr Virus Genomes Reveal Population Structure and Type 1 Association with Endemic Burkitt Lymphoma.

Endemic Burkitt lymphoma (eBL), the most prevalent pediatric cancer in sub-Saharan Africa, is distinguished by its inclusion of Epstein-Barr virus (EBV). In order to better understand the impact of EBV variation in eBL tumorigenesis, we improved viral DNA enrichment methods and generated a total of 98 new EBV genomes from both eBL cases (n = 58) and healthy controls (n = 40) residing in the same geographic region in Kenya. Using our unbiased methods, we found that EBV type 1 was significantly more prevalent in eBL patients (74.5%) than in healthy children (47.5%) (odds ratio = 3.24, 95% confidence interval = 1.36 to 7.71, P = 0.007), as opposed to similar proportions in both groups. Controlling for EBV type, we also performed a genome-wide association study identifying six nonsynonymous variants in the genes EBNA1, EBNA2, BcLF1, and BARF1 that were enriched in eBL patients. In addition, viruses isolated from plasma of eBL patients were identical to their tumor counterparts consistent with circulating viral DNA originating from the tumor. We also detected three intertypic recombinants carrying type 1 EBNA2 and type 2 EBNA3 regions, as well as one novel genome with a 20-kb deletion, resulting in the loss of multiple lytic and virion genes. Comparing EBV types, viral genes displayed differential variation rates as type 1 appeared to be more divergent, while type 2 demonstrated novel substructures. Overall, our findings highlight the complexities of the EBV population structure and provide new insight into viral variation, potentially deepening our understanding of eBL oncogenesis.IMPORTANCE Improved viral enrichment methods conclusively demonstrate EBV type 1 to be more prevalent in eBL patients than in geographically matched healthy controls, which previously underrepresented the prevalence of EBV type 2. Genome-wide association analysis between cases and controls identifies six eBL-associated nonsynonymous variants in EBNA1, EBNA2, BcLF1, and BARF1 genes. Analysis of population structure reveals that EBV type 2 exists as two genomic subgroups and was more commonly found in female than in male eBL patients.
Authors
Kaymaz, Y; Oduor, CI; Aydemir, O; Luftig, MA; Otieno, JA; Ong'echa, JM; Bailey, JA; Moormann, AM
MLA Citation
Kaymaz, Yasin, et al. “Epstein-Barr Virus Genomes Reveal Population Structure and Type 1 Association with Endemic Burkitt Lymphoma.J Virol, vol. 94, no. 17, Aug. 2020. Pubmed, doi:10.1128/JVI.02007-19.
URI
https://scholars.duke.edu/individual/pub1448854
PMID
32581102
Source
pubmed
Published In
J Virol
Volume
94
Published Date
DOI
10.1128/JVI.02007-19

Reprogramming of cellular metabolic pathways by human oncogenic viruses.

Oncogenic viruses, like all viruses, relies on host metabolism to provide the metabolites and energy needed for virus replication. Many DNA tumor viruses and retroviruses will reprogram metabolism during infection. Additionally, some viral oncogenes may alter metabolism independent of virus replication. Virus infection and cancer development share many similarities regarding metabolic reprogramming as both processes demand increased metabolic activity to produce biomass: cell proliferation in the case of cancer and virion production in the case of infection. This review discusses the parallels in metabolic reprogramming between human oncogenic viruses and oncogenesis.
Authors
Purdy, JG; Luftig, MA
MLA Citation
Purdy, John G., and Micah A. Luftig. “Reprogramming of cellular metabolic pathways by human oncogenic viruses.Curr Opin Virol, vol. 39, Dec. 2019, pp. 60–69. Pubmed, doi:10.1016/j.coviro.2019.11.002.
URI
https://scholars.duke.edu/individual/pub1422428
PMID
31766001
Source
pubmed
Published In
Curr Opin Virol
Volume
39
Published Date
Start Page
60
End Page
69
DOI
10.1016/j.coviro.2019.11.002

The whole-genome landscape of Burkitt lymphoma subtypes.

Burkitt lymphoma (BL) is an aggressive, MYC-driven lymphoma comprising 3 distinct clinical subtypes: sporadic BLs that occur worldwide, endemic BLs that occur predominantly in sub-Saharan Africa, and immunodeficiency-associated BLs that occur primarily in the setting of HIV. In this study, we comprehensively delineated the genomic basis of BL through whole-genome sequencing (WGS) of 101 tumors representing all 3 subtypes of BL to identify 72 driver genes. These data were additionally informed by CRISPR screens in BL cell lines to functionally annotate the role of oncogenic drivers. Nearly every driver gene was found to have both coding and non-coding mutations, highlighting the importance of WGS for identifying driver events. Our data implicate coding and non-coding mutations in IGLL5, BACH2, SIN3A, and DNMT1. Epstein-Barr virus (EBV) infection was associated with higher mutation load, with type 1 EBV showing a higher mutational burden than type 2 EBV. Although sporadic and immunodeficiency-associated BLs had similar genetic profiles, endemic BLs manifested more frequent mutations in BCL7A and BCL6 and fewer genetic alterations in DNMT1, SNTB2, and CTCF. Silencing mutations in ID3 were a common feature of all 3 subtypes of BL. In vitro, mass spectrometry-based proteomics demonstrated that the ID3 protein binds primarily to TCF3 and TCF4. In vivo knockout of ID3 potentiated the effects of MYC, leading to rapid tumorigenesis and tumor phenotypes consistent with those observed in the human disease.
Authors
Panea, RI; Love, CL; Shingleton, JR; Reddy, A; Bailey, JA; Moormann, AM; Otieno, JA; Ong'echa, JM; Oduor, CI; Schroeder, KMS; Masalu, N; Chao, NJ; Agajanian, M; Major, MB; Fedoriw, Y; Richards, KL; Rymkiewicz, G; Miles, RR; Alobeid, B; Bhagat, G; Flowers, CR; Ondrejka, SL; Hsi, ED; Choi, WWL; Au-Yeung, RKH; Hartmann, W; Lenz, G; Meyerson, H; Lin, Y-Y; Zhuang, Y; Luftig, MA; Waldrop, A; Dave, T; Thakkar, D; Sahay, H; Li, G; Palus, BC; Seshadri, V; Kim, SY; Gascoyne, RD; Levy, S; Mukhopadyay, M; Dunson, DB; Dave, SS
MLA Citation
Panea, Razvan I., et al. “The whole-genome landscape of Burkitt lymphoma subtypes.Blood, vol. 134, no. 19, Nov. 2019, pp. 1598–607. Pubmed, doi:10.1182/blood.2019001880.
URI
https://scholars.duke.edu/individual/pub1415067
PMID
31558468
Source
pubmed
Published In
Blood
Volume
134
Published Date
Start Page
1598
End Page
1607
DOI
10.1182/blood.2019001880

Identification of Host Biomarkers of Epstein-Barr Virus Latency IIb and Latency III.

Deciphering the molecular pathogenesis of virally induced cancers is challenging due, in part, to the heterogeneity of both viral gene expression and host gene expression. Epstein-Barr virus (EBV) is a ubiquitous herpesvirus prevalent in B-cell lymphomas of immune-suppressed individuals. EBV infection of primary human B cells leads to their immortalization into lymphoblastoid cell lines (LCLs), serving as a model of these lymphomas. In previous studies, reports from our laboratory have described a temporal model for immortalization with an initial phase characterized by expression of Epstein-Barr nuclear antigens (EBNAs), high levels of c-Myc activity, and hyperproliferation in the absence of the latent membrane proteins (LMPs), called latency IIb. This is followed by the long-term outgrowth of LCLs expressing the EBNAs along with the LMPs, particularly NFκB-activating LMP1, defining latency III. However, LCLs express a broad distribution of LMP1 such that a subset of these cells express LMP1 at levels similar to those seen in latency IIb, making it difficult to distinguish these two latency states. In this study, we performed mRNA sequencing (mRNA-Seq) on early EBV-infected latency IIb cells and latency III LCLs sorted by NFκB activity. We found that latency IIb transcriptomes clustered independently from latency III independently of NFκB. We identified and validated mRNAs defining these latency states. Indeed, we were able to distinguish latency IIb cells from LCLs expressing low levels of LMP1 using multiplex RNA-fluorescence in situ hybridization (RNA-FISH) targeting EBV EBNA2 or LMP1 and human CCR7 or MGST1 This report defines latency IIb as a bona fide latency state independent from latency III and identifies biomarkers for understanding EBV-associated tumor heterogeneity.IMPORTANCE EBV is a ubiquitous pathogen, with >95% of adults harboring a life-long latent infection in memory B cells. In immunocompromised individuals, latent EBV infection can result in lymphoma. The established expression profile of these lymphomas is latency III, which includes expression of all latency genes. However, single-cell analysis of EBV latent gene expression in these lymphomas suggests heterogeneity where most cells express the transcription factor, EBNA2, and only a fraction of the cells express membrane protein LMP1. Our work describes an early phase after infection where the EBNAs are expressed without LMP1, called latency IIb. However, LMP1 levels within latency III vary widely, making these states hard to discriminate. This may have important implications for therapeutic responses. It is crucial to distinguish these states to understand the molecular pathogenesis of these lymphomas. Ultimately, better tools to understand the heterogeneity of these cancers will support more-efficacious therapies in the future.
Authors
Messinger, JE; Dai, J; Stanland, LJ; Price, AM; Luftig, MA
MLA Citation
Messinger, Joshua E., et al. “Identification of Host Biomarkers of Epstein-Barr Virus Latency IIb and Latency III.Mbio, vol. 10, no. 4, July 2019. Pubmed, doi:10.1128/mBio.01006-19.
URI
https://scholars.duke.edu/individual/pub1395720
PMID
31266868
Source
pubmed
Published In
Mbio
Volume
10
Published Date
DOI
10.1128/mBio.01006-19

c-Myc Represses Transcription of Epstein-Barr Virus Latent Membrane Protein 1 Early after Primary B Cell Infection.

Recent evidence has shown that the Epstein-Barr virus (EBV) oncogene LMP1 is not expressed at high levels early after EBV infection of primary B cells, despite its being essential for the long-term outgrowth of immortalized lymphoblastoid cell lines (LCLs). In this study, we found that expression of LMP1 increased 50-fold between 7 days postinfection and the LCL state. Metabolic labeling of nascent transcribed mRNA indicated that this was primarily a transcription-mediated event. EBNA2, the key viral transcription factor regulating LMP1, and CTCF, an important chromatin insulator, were recruited to the LMP1 locus similarly early and late after infection. However, the activating histone H3K9Ac mark was enriched at the LMP1 promoter in LCLs relative to that in infected B cells early after infection. We found that high c-Myc activity in EBV-infected lymphoma cells as well as overexpression of c-Myc in an LCL model system repressed LMP1 transcription. Finally, we found that chemical inhibition of c-Myc both in LCLs and early after primary B cell infection increased LMP1 expression. These data support a model in which high levels of endogenous c-Myc activity induced early after primary B cell infection directly repress LMP1 transcription.IMPORTANCE EBV is a highly successful pathogen that latently infects more than 90% of adults worldwide and is also causally associated with a number of B cell malignancies. During the latent life cycle, EBV expresses a set of viral oncoproteins and noncoding RNAs with the potential to promote cancer. Critical among these is the viral latent membrane protein LMP1. Prior work suggests that LMP1 is essential for EBV to immortalize B cells, but our recent work indicates that LMP1 is not produced at high levels during the first few weeks after infection. Here we show that transcription of the LMP1 gene can be negatively regulated by a host transcription factor, c-Myc. Ultimately, understanding the regulation of EBV oncogenes will allow us to better treat cancers that rely on these viral products for survival.
Authors
Price, AM; Messinger, JE; Luftig, MA
MLA Citation
Price, Alexander M., et al. “c-Myc Represses Transcription of Epstein-Barr Virus Latent Membrane Protein 1 Early after Primary B Cell Infection.J Virol, vol. 92, no. 2, Jan. 2018. Pubmed, doi:10.1128/JVI.01178-17.
URI
https://scholars.duke.edu/individual/pub1284410
PMID
29118124
Source
pubmed
Published In
J Virol
Volume
92
Published Date
DOI
10.1128/JVI.01178-17

Research Areas:

3' Untranslated Regions
Actin Cytoskeleton
Adult
Algorithms
Animals
Antibodies, Monoclonal
Apoptosis
Automation
B-Lymphocytes
Base Sequence
Biological Markers
Cell Adhesion Molecules
Cell Cycle Proteins
Cell Growth Processes
Cell Line
Cell Line, Transformed
Cell Line, Tumor
Cell Nucleus
Cell Proliferation
Cell Survival
Cell Transformation, Neoplastic
Cell Transformation, Viral
Cells, Cultured
Chromatin Immunoprecipitation
Clone Cells
Coculture Techniques
Crystallography, X-Ray
DNA Damage
DNA Mutational Analysis
DNA, Neoplasm
DNA-Binding Proteins
Epithelial Cells
Epstein-Barr Virus Infections
Epstein-Barr Virus Nuclear Antigens
Epstein-barr Virus
Exome
Feeder Cells
Gene Expression
Gene Expression Profiling
Gene Expression Regulation
Gene Library
Gene Order
Genes, Reporter
Genes, cdc
Genetic Heterogeneity
Genetic Variation
Genetic Vectors
HIV Envelope Protein gp41
HIV-1
Herpesvirus 1, Human
Herpesvirus 4, Human
High-Throughput Nucleotide Sequencing
Host-Pathogen Interactions
Humans
Hydrophobic and Hydrophilic Interactions
Interleukin-1 Receptor-Associated Kinases
Leucine
Leukemia, Lymphocytic, Chronic, B-Cell
Luciferases
Lymphocyte Activation
Lymphoma, B-Cell
Lymphoma, Large B-Cell, Diffuse
Lymphoproliferative Disorders
Macrophages
Mass Spectrometry
Mice
MicroRNAs
Microscopy, Electron
Models, Biological
Models, Molecular
Molecular Sequence Data
Molecular Targeted Therapy
Molecular Weight
Mutation
NF-kappa B
Neutralization Tests
Oligonucleotide Array Sequence Analysis
Oncogenes
Oncogenic Viruses
Peptide Fragments
Phosphatidylinositol 3-Kinases
Phosphorylation
Piperazines
Protein Binding
Protein Conformation
Protein Kinases
Protein Structure, Quaternary
Protein Structure, Secondary
Protein Structure, Tertiary
Protein Transport
Protein-Serine-Threonine Kinases
Proteins
Proto-Oncogene Proteins c-kit
RNA
RNA, Messenger
RNA, Viral
Real-Time Polymerase Chain Reaction
Receptor, Platelet-Derived Growth Factor alpha
Receptors, Virus
Recombinant Fusion Proteins
Recombinant Proteins
Retroviridae
Reverse Transcriptase Polymerase Chain Reaction
Sequence Analysis, RNA
Sequence Homology, Nucleic Acid
Signal Transduction
Structure-Activity Relationship
TNF Receptor-Associated Factor 6
Transcription Factors
Transduction, Genetic
Transfection
Tryptophan
Tumor Cells, Cultured
Tumor Suppressor Protein p53
Tumor Suppressor Proteins
Tumor Virus Infections
Up-Regulation
Vero Cells
Viral Envelope Proteins
Viral Matrix Proteins
Viral Proteins
Virus Internalization
Virus Latency
Virus Replication
epstein-barr virus