Emily Hodges, Ph.D.
- Assistant Professor of Biochemistry
The genetic and epigenetic determinants of disease susceptibility and progression remain poorly understood for many types of sporadic hematological cancers. This is especially true for cases with mixed clinical outcomes such as chronic lymphocytic leukemia (CLL). Recent studies have shown that disease associated sequence variants frequently occur in non-protein-coding regions of the human genome, often disrupting functional gene regulatory elements. Through utilization of genomic and computational approaches, our research addresses the contribution and functional variation of non-coding gene regulatory elements to different types of leukemia, complementing current efforts to better understand the molecular basis of cancer. This strategy may uncover alternative routesto identify cancer susceptibility loci and targets for drug intervention. An important aspect of my research is to understand how DNA methylation influences the behaviors of gene regulatory elements in normal cell-types and how this epigenetic mark is disrupted in cancer. Therefore, we study mechanisms by which DNA methylation states are established in differentiating cells and the degree to which DNA methylation itself regulates gene expression.
- Research Fellow, Cold Spring Harbor Laboratory, New York
- Ph.D. Karolinska Institute, Stockholm, Sweden
- B.A. Rhodes College, Memphis, TN
DNA methylation and non-coding gene regulatory variation in evolution, development and disease
Research in the Hodges Lab strives to understand the relationship between genetics and epigenetics, and how they together influence gene regulation differences, phenotypic diversity, and susceptibility to disease. Our work aims to understand the relationship between DNA methylation and gene regulation, particularly with respect to the gene regulatory activity of non-coding functional elements. We study this relationship on two levels; first, we are interested in how DNA methylation states are established in differentiating cells. Second, we are interested in the relationship between genotype and DNA methylation state (epitype).
- Hodges E. Sequencing in High Definition Drives a Changing Worldview of the Epigenome. Cold Spring Harb Perspect Med. 2019 Jun 6/3/2019; 9(6): PMID: 30201789, PII: cshperspect.a033076, DOI: 10.1101/cshperspect.a033076, ISSN: 2157-1422.
- Liu J, Banerjee A, Herring CA, Attalla J, Hu R, Xu Y, Shao Q, Simmons AJ, Dadi PK, Wang S, Jacobson DA, Liu B, Hodges E, Lau KS, Gu G. Neurog3-Independent Methylation Is the Earliest Detectable Mark Distinguishing Pancreatic Progenitor Identity. Dev. Cell. 2019 Jan 1/7/2019; 48(1): 49-63.e7. PMID: 30620902, PMCID: PMC6327977, PII: S1534-5807(18)31032-3, DOI: 10.1016/j.devcel.2018.11.048, ISSN: 1878-1551.
- Boothby MR, Hodges E, Thomas JW. Molecular regulation of peripheral B cells and their progeny in immunity. Genes Dev. 2019 Jan 1/1/2019; 33(1-2): 26-48. PMID: 30602439, PMCID: PMC6317321, PII: 33/1-2/26, DOI: 10.1101/gad.320192.118, ISSN: 1549-5477.
- Qu J, Hodges E, Molaro A, Gagneux P, Dean MD, Hannon GJ, Smith AD. Evolutionary expansion of DNA hypomethylation in the mammalian germline genome. Genome Res [print-electronic]. 2018 Feb; 28(2): 145-58. PMID: 29259021, PMCID: PMC5793779, PII: gr.225896.117, DOI: 10.1101/gr.225896.117, ISSN: 1549-5469.
- Stengel KR, Barnett KR, Wang J, Liu Q, Hodges E, Hiebert SW, Bhaskara S. Deacetylase activity of histone deacetylase 3 is required for productive VDJ recombination and B-cell development. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2017 Aug 8/8/2017; 114(32): 8608-13. PMID: 28739911, PMCID: PMC5559004, PII: 1701610114, DOI: 10.1073/pnas.1701610114, ISSN: 1091-6490.
- Chang D, Knapp M, Enk J, Lippold S, Kircher M, Lister A, MacPhee RD, Widga C, Czechowski P, Sommer R, Hodges E, Stümpel N, Barnes I, Dalén L, Derevianko A, Germonpré M, Hillebrand-Voiculescu A, Constantin S, Kuznetsova T, Mol D, Rathgeber T, Rosendahl W, Tikhonov AN, Willerslev E, Hannon G, Lalueza-Fox C, Joger U, Poinar H, Hofreiter M, Shapiro B. The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis. Sci Rep. 2017 Mar 3/22/2017; 7: 44585. PMID: 28327635, PII: srep44585, DOI: 10.1038/srep44585, ISSN: 2045-2322.
- McFadden DG, Politi K, Bhutkar A, Chen FK, Song X, Pirun M, Santiago PM, Kim-Kiselak C, Platt JT, Lee E, Hodges E, Rosebrock AP, Bronson RT, Socci ND, Hannon GJ, Jacks T, Varmus H. Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2016 Oct 10/18/2016; 113(42): E6409-E6417. PMID: 27702896, PMCID: PMC5081629, PII: 1613601113, DOI: 10.1073/pnas.1613601113, ISSN: 1091-6490.
- Dos Santos CO, Dolzhenko E, Hodges E, Smith AD, Hannon GJ. An epigenetic memory of pregnancy in the mouse mammary gland. Cell Rep [print-electronic]. 2015 May 5/19/2015; 11(7): 1102-9. PMID: 25959817, PMCID: PMC4439279, PII: S2211-1247(15)00390-3, DOI: 10.1016/j.celrep.2015.04.015, ISSN: 2211-1247.
- Malaspinas AS, Lao O, Schroeder H, Rasmussen M, Raghavan M, Moltke I, Campos PF, Sagredo FS, Rasmussen S, Gonçalves VF, Albrechtsen A, Allentoft ME, Johnson PL, Li M, Reis S, Bernardo DV, DeGiorgio M, Duggan AT, Bastos M, Wang Y, Stenderup J, Moreno-Mayar JV, Brunak S, Sicheritz-Ponten T, Hodges E, Hannon GJ, Orlando L, Price TD, Jensen JD, Nielsen R, Heinemeier J, Olsen J, Rodrigues-Carvalho C, Lahr MM, Neves WA, Kayser M, Higham T, Stoneking M, Pena SD, Willerslev E. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil [letter]. Curr. Biol [print-electronic]. 2014 Nov 11/3/2014; 24(21): R1035-7. PMID: 25455029, PMCID: PMC4370112, PII: S0960-9822(14)01274-3, DOI: 10.1016/j.cub.2014.09.078, ISSN: 1879-0445.
- Molaro A, Falciatori I, Hodges E, Aravin AA, Marran K, Rafii S, McCombie WR, Smith AD, Hannon GJ. Two waves of de novo methylation during mouse germ cell development. Genes Dev. 2014 Jul 7/15/2014; 28(14): 1544-9. PMID: 25030694, PMCID: PMC4102761, PII: 28/14/1544, DOI: 10.1101/gad.244350.114, ISSN: 1549-5477.