• Title Professor of Biology, Medicine, and Biomedical Engineering; Program in Bioinformatics
  • Education PhD, Harvard University
  • Phone 617-353-7402
  • Area of Interest Genomic and epigenetic mechanisms controlling liver gene expression; molecular endocrinology and cell signaling through transcriptional networks; role of angiogenesis and innate immune system in cancer therapy and pharmacology; nuclear receptors and responses to environmental chemicals
  • CV

***NEW Postdoctoral Research Openings***

Current Research

Our research program encompasses three major projects, investigating these questions:

1. How do hormone regulatory circuits, epigenetic modifiers and long non-coding RNA genes interact to regulate complex patterns of gene expression in mammalian tissues?

2. By which mechanisms does exposure to environmental chemicals with hormone-like properties reprogram developing tissues, leading to persistent dysregulation of gene expression at adulthood and an increase in adult onset disease?

3. Can improved strategies for cancer treatment be devised through a better understanding of the effects of cancer chemotherapy on host-tumor interactions and immune responses to drug treatment?

Mechanisms of hormone-regulated sex differences in liver gene expression – This project aims to elucidate global (genome-wide) transcriptional and epigenetic networks that dictate the sex-differential expression of more than 1,000 genes in mammalian liver; these sex-differential gene profiles have been linked to clinically relevant sex differences in hepatic drug metabolism, lipid metabolic profiles, and cardiovascular disease risk. Our current research efforts use both mouse models and cell culture studies in combination with powerful next generation sequencing technologies and in-house bioinformatics analysis to elucidate global regulatory mechanisms. The technologies we employ include: transcriptional profiling at the single cell level (scRNA-seq) combined with chromatin accessibility analysis, to identify open chromatin (regulatory) regions in the genome (ATAC-seq, DNase-seq); massively parallel reporter assays, to elucidate functional enhancers (STARR-seq); and histone mark and transcription factor location analysis (ChIP-seq), to deduce chromatin states. In addition, we implement CRISPR/dCas9-based epigenetic remodeling in mouse liver in vivo to probe the role of novel long non-coding RNA (lncRNA) genes in the sex-differential regulatory networks. The rich, genome wide data sets that we develop are analyzed to discover the unique chromatin states that characterize genes showing sex differences in their expression, and the epigenetic mechanisms that establish these states; and gene regulatory circuits associated with these sex-dependent chromatin states, through which the temporal pattern of pituitary growth hormone secretion either masculinizes (pulsatile hormone stimulation) or, alternatively, feminizes gene expression in the liver (persistent hormone stimulation), with major impact on liver disease susceptibility and development.

Epigenomic effects of environmental chemical exposures – We are studying the genomic and epigenetic actions of environmental chemicals, which can induce developmental and adult disease-associated toxicities in humans and exposed wildlife. For example, prenatal and neonatal exposure to estrogen-like environmental chemicals can induce major structural and functional abnormalities in sensitive tissues, such as the liver, and thereby increase susceptibility to adult onset of disease, such as fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), and hepatocellular carcinoma (HCC). However, the molecular mechanisms that underlie the early developmental lesions and that lead to these developmental and disease-associated defects and adult pathophysiology are poorly understood. We are presently investigating the hypothesis that in utero exposure to environmental chemicals alters the expression of epigenetic regulators, including xenochemical-responsive long non-coding RNA (lncRNA) genes that confer life-long changes in expression of key genes controlling tissue development. Our studies primarily use the mouse model, and focus on environmental chemical agonists of several transcription factors that belong to the nuclear receptor (NR) superfamily, including the nuclear receptors CAR, PRX and PPAR, which also serve as targets for many therapeutic drugs.

Cancer therapy and the immune system – Recent advances in our understanding of host-tumor interactions have provided new opportunities to improve cancer treatment using drugs administered through novel treatment schedules, such as metronomic chemotherapy, which we have discovered can activate interferon and other innate immune-signaling cascades resulting in potent, anti-tumor immune responses. We have found using mouse models of glioma and breast cancer that single agent chemotherapy, based on cyclophosphamide administered on a 6-day repeating metronomic schedule, can activate immunogenic tumor cell death that is CD8-T cell dependent and leads to a major increase in therapeutic response. Further, we have found that the increase in therapeutic efficacy is largely due to cyclophosphamide activation of tumor cell autonomous type-I interferon signaling, with release of soluble factors that activate interferon-stimulated genes in both tumor cells and tumor-infiltrating immune cells. Important goals of this project include: the discovery of the tumor cell-centric mechanisms through which cyclophosphamide activates interferon and other innate immune response pathways; identification of deficiencies in immune-unresponsive patient-derived tumor models; and development of efficacious immunogenic chemo-immunotherapies that combine metronomic cyclophosphamide scheduling with immunotherapies that circumvent block in immune responsiveness.

Selected Publications

  • Hao P, Waxman DJ (2021). STAT5 regulation of sex-dependent hepatic CpG methylation at distal regulatory elements mapping to sex-biased genes. Mol Cell Biol (2021) 41(2):e00166-20. doi: 10.1128/MCB.00166-20. PMID: 33199496.
  • Goldfarb CN, Waxman DJ (2021). Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs. BMC Genomics 22(1):212. doi: 10.1186/s12864-021-07478-5. PMID: 33761883.
  • Melia T, Waxman DJ (2020). Genetic factors contributing to extensive variability of sex-specific hepatic gene expression in Diversity Outbred mice. PLoS One 15(12):e0242665. doi: 10.1371/journal.pone.0242665. PMID: 33264334.
  • Brocker CN, Kim D, Melia T, Karri K, Velenosi TJ, Takahashi S, Aibara D, Bonzo JA, Levi M, Waxman DJ, Gonzalez FJ. (2020) Long non-coding RNA Gm15441 attenuates hepatic inflammasome activation in response to PPARA agonism and fasting. Nat Commun 11(1):5847. doi: 10.1038/s41467-020-19554-7. PMID: 33203882.
  • Matthews BJ, Waxman DJ (2020) Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver. Epigenetics & Chromatin 13 (1): 30. DOI: 10.1186/s13072-020-00350-y. PMID: 32680543.
  • Lau-Corona D, Bae WK, Hennighausen L, Waxman DJ (2020) Sex-biased genetic programs in liver metabolism and liver fibrosis are controlled by EZH1 and EZH2. PLoS Genetics 16 (5): e1008796. DOI: 10.1371/journal.pgen.1008796. eCollection 2020 May. PMID: 32428001.
  • Karri K, Waxman DJ (2020) Widespread Dysregulation of Long Noncoding Genes Associated With Fatty Acid Metabolism, Cell Division, and Immune Response Gene Networks in Xenobiotic-exposed Rat Liver. Toxicol Sci 174 (2): 291-310. DOI: 10.1093/toxsci/kfaa001. PMID: 31926019.
  • Du B, Waxman DJ (2020) Medium dose intermittent cyclophosphamide induces immunogenic cell death and cancer cell autonomous type I interferon production in glioma models. Cancer Lett. PII: S0304-3835(19)30580-4. DOI: 10.1016/j.canlet.2019.11.025. [Epub ahead of print] PMID: 31765733.
  • Rampersaud A, Lodato NJ, Shin A, Waxman DJ (2019) Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR. Toxicol Sci. PII: kfz148. DOI: 10.1093/toxsci/kfz148. PMID: 31236583.
  • Matthews BJ, Waxman DJ (2018) Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver. Elife. PII: e34077. DOI: 10.7554/eLife.34077. PubMed PMID: 29757144.

Courses Taught:

  • BI 556 Membrane Biochemistry and Cell Signaling
  • BI 735 Advanced Cell Biology

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