About

John M. Essigmann is a Professor of Toxicology and Biological Engineering and a Professor of Chemistry at MIT. His research focuses on how cells respond to DNA damaging agents, including radiation, chemicals, and antitumor agents, which cause chemical alterations in the genome to form covalent adducts. His work investigates how repair enzymes remove structural damage from DNA and how adducts that evade repair can lead to cell death, mutations, and cancer. His studies on mutagenesis involve synthesizing oligonucleotides with specific DNA adducts, inserting them into viral genomes, and analyzing mutation patterns after DNA replication and repair processes in cells. Additionally, Essigmann's research on antitumor drug mechanisms includes studying cis-diamminedichloroplatinum(II) (cisplatin), which binds to DNA and forms adducts that interfere with tumor cell DNA replication and transcription. He has discovered that the transcription factor hUBF binds tightly to cisplatin DNA adducts, potentially disrupting gene transcription. His laboratory also works on the synthesis of programmable therapeutics, creating bifunctional molecules that target overexpressed proteins in tumors, such as steroid receptors, to hinder DNA repair and promote cell death selectively in cancer cells. These efforts aim to develop targeted cancer treatments, with promising molecules evolved for breast and prostate cancers, including strategies to overcome typical resistance mechanisms in prostate cancer.

Research topics

• Biology
• Genetics
• Medicine
• Molecular biology
• Cell biology
• Cancer research
• Chemistry
• Pathology
• Computational biology

Selected publications

• Sex and Alkyladenine DNA Glycosylase Expression are Key Susceptibility Factors for NDMA-induced Mutations, Toxicity, and Cancer

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-14 · 2 citations

  preprintOpen access

  ABSTRACT N -Nitrosodimethylamine (NDMA) is present in food, water, and drugs and is considered a probable human carcinogen by the International Agency for Research on Cancer. The mechanism of action of NDMA involves the generation of carcinogenic methyl lesions such as 3-methyladenine (3MeA) on DNA bases. Alkyladenine DNA Glycosylase (AAG) removes 3MeA to initiate Base Excision Repair, leaving an intermediary lesion that is subsequently resolved by backbone cleavage, nucleotide insertion, and backbone ligation. The intermediate steps following lesion removal produce potentially toxic and mutagenic single-strand DNA breaks. Here, we explored differences between males and females regarding downstream DNA damage, toxicity, mutations and cancer arising from 3MeA in the livers of WT, Aag -/- , and Aag -overexpressing ( AagTg ) mice. We found that males were more susceptible to NDMA-induced mutations (WT and Aag -/- ) and cancer (all genotypes). In contrast, AagTg females were more prone than males to micronucleus induction. As we showed in our prior analyses where data were pooled for males and females, Aag -/- mice were significantly more susceptible to NDMA-induced mutations and cancer, and AagTg mice displayed significantly greater toxicity. Building on these findings, our analyses of sex-related differences show that Aag deficiency and maleness are both susceptibility factors for NDMA-induced liver cancer, while Aag overexpression drives toxicity, potentially with a greater effect on females. By assessing differences between males and females, this study reveals a deeper mechanistic understanding of the underpinnings for a well-known increased risk of liver cancer in men versus women by demonstrating a higher susceptibility of male mice to both mutations and cancer.

  PublisherOA PDFDOI

• Persistent interferon signaling and clonal expansion mark early events in DNA methylation damage-induced liver cancer

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-03 · 2 citations

  preprintOpen access

  -methylguanine methyltransferase (MGMT). To elucidate mechanisms of NDMA-induced liver cancer progression, we performed longitudinal analyses of phenomic, transcriptomic, and phosphoproteomic changes in wild-type and MGMT-deficient mice, observing amplified responses in the deficient genotype. Early molecular rewiring indicative of a DNA damage response was detected by phosphoproteomic and transcriptomic profiling within days post-exposure. Transcriptomic analyses identified a persistent and robust interferon response as the dominant activated pathway. This chronic interferon signaling, which remained unresolved, correlated with extensive clonal expansion, an early hallmark of oncogenesis. Spatial transcriptomics further revealed pathway alterations favoring tumorigenesis within clonally expanded cells. These findings delineate the cascade of molecular events triggered by acute early-life NDMA exposure, culminating in cancer development months later. Our study unveils potential predictive biomarkers and strategies for disease mitigation.

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• Structurally Similar Mycotoxins Aflatoxin B1 and Sterigmatocystin Trigger Different and Distinctive High-Resolution Mutational Spectra in Mammalian Cells

  Toxins · 2025-02-27

  articleOpen accessSenior authorCorresponding

  Aflatoxin B1 (AFB1) and sterigmatocystin (ST) are mycotoxins that pose significant threats to human and animal health owing to their mutagenic, carcinogenic, and toxic properties. They are structurally similar and widely believed to exert their biological effects via the generation of DNA-damaging epoxides at their respective terminal furan rings. Despite structural identity in the warhead portion of each toxin, this work shows that distal parts of each molecule are responsible for the distinctive mutational fingerprints seen in gptΔ C57BL/6J mouse embryo fibroblasts (MEFs). The two toxins differ structurally in the puckered cyclopentenone ring of AFB1 and in the planar xanthone functionality of ST. While both toxins mainly induce GC→TA mutations, the aforementioned differences in structure apparently trigger unique patterns of mutations, as revealed by high-resolution duplex sequencing of MEF genomes. AFB1 is more mutagenic than ST and displays its transversion mutations in a pattern with primary and secondary hotspots (underscored) in 5′-CGC-3′ and 5′-CGG-3′ contexts, respectively. ST displays a modest 5′-CGG-3′ hotspot while its other GC→TA transversions are more uniformly distributed in a pattern resembling established oxidative stress mutational spectra. This research delineates the mutational spectra of AFB1 and ST, establishing these patterns as possible early-onset biomarkers of exposure.

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• Systems analysis uncovers early temozolomide responses and peptide antigens in glioblastoma

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-12

  preprint

  Temozolomide (TMZ) is the standard treatment for nearly all glioblastoma (GBM) patients, as it is the only chemotherapy shown to extend overall survival. However, this benefit is limited to a few months, underscoring the need for combination strategies to improve its efficacy. While TMZ-induced DNA damage can both mediate cytotoxicity and promote resistance, DNA damage more broadly can also stimulate immune activation. To evaluate its immunomodulatory potential, we characterized the previously unexplored early, cell-intrinsic consequences of TMZ in GBM cells, spanning DNA damage, stress responses, and antigen presentation. A multi-omics approach combining RNA sequencing and quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) profiled changes in gene expression, nascent protein translation, steady-state protein levels, kinase-substrate phosphorylation patterns, and MHC-I peptide presentation in GBM cells within 72 hours of TMZ exposure. This analysis revealed rapid activation of DNA damage signaling and p53-associated stress pathways, alongside dynamic changes in protein synthesis and antigen presentation. A set of TMZ treatment-associated peptide antigens (TAPAs) was identified, including peptides derived from stress response proteins, phosphorylated MHC-I peptides, and those induced by other genotoxic treatments such as radiation. Several of these peptides were also detected in recurrent GBM patient tumors. Our findings suggest that TMZ not only triggers early adaptive and potentially resistance-associated stress programs but may also enhance the immune visibility of GBM cells. These data highlight potential windows for combination therapies with TMZ that bolster immune recognition of GBM, while the systems approach provides a framework to examine how genotoxic therapies across cancers alter tumor immunogenicity.

  PublisherDOI

• Colorimetric Detection of Aqueous <i>N</i>-Nitrosodimethylamine via Photonitrosation of a Naphtholsulfonate Indicator

  ACS Sensors · 2024-08-21 · 7 citations

  articleOpen access

  N-Nitrosamines are contaminants found throughout the environment, including in drinking water, and many nitrosamines are likely potent carcinogens. Correspondingly, there is a need for rapid and cost-effective in-field detection methods that can provide timely information about their contamination levels in water. This study details a colorimetric assay for detecting aqueous N-nitrosodimethylamine (NDMA) by photochemical nitrosation of a commercial naphtholsulfonate, to offer an attractive alternative to traditional laboratory-based analysis. The resulting naphthoquinone-oxime coordinates to aqueous iron(II) ions to form a green complex, allowing for direct visual detection. Characterization via Mössbauer and electron paramagnetic resonance (EPR) spectroscopy, alongside single-crystal structure determination, provides comprehensive structure information on the iron indicator complex. Optimization of detection conditions, including UV irradiation and response times, led to an improved colorimetric detection method with a limit of detection of 0.66 ppm for NDMA. The practical applicability and selectivity of this colorimetric detection scheme make it a promising candidate for the development of field-deployable sensors for NDMA in environmental water samples.

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• Stable Interstrand Cross-Links Generated from the Repair of 1,<i>N</i>⁶-Ethenoadenine in DNA by α-Ketoglutarate/Fe(II)-Dependent Dioxygenase ALKBH2

  Journal of the American Chemical Society · 2024-04-04 · 4 citations

  articleOpen access

  DNA cross-links severely challenge replication and transcription in cells, promoting senescence and cell death. In this paper, we report a novel type of DNA interstrand cross-link (ICL) produced as a side product during the attempted repair of 1,N6-ethenoadenine (εA) by human α-ketoglutarate/Fe(II)-dependent enzyme ALKBH2. This stable/nonreversible ICL was characterized by denaturing polyacrylamide gel electrophoresis analysis and quantified by high-resolution LC–MS in well-matched and mismatched DNA duplexes, yielding 5.7% as the highest level for cross-link formation. The binary lesion is proposed to be generated through covalent bond formation between the epoxide intermediate of εA repair and the exocyclic N6-amino group of adenine or the N4-amino group of cytosine residues in the complementary strand under physiological conditions. The cross-links occur in diverse sequence contexts, and molecular dynamics simulations rationalize the context specificity of cross-link formation. In addition, the cross-link generated from attempted εA repair was detected in cells by highly sensitive LC–MS techniques, giving biological relevance to the cross-link adducts. Overall, a combination of biochemical, computational, and mass spectrometric methods was used to discover and characterize this new type of stable cross-link both in vitro and in human cells, thereby uniquely demonstrating the existence of a potentially harmful ICL during DNA repair by human ALKBH2.

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• 5-Chloro-2′-deoxycytidine Induces a Distinctive High-Resolution Mutational Spectrum of Transition Mutations In Vivo

  Chemical Research in Toxicology · 2024-02-23 · 4 citations

  articleOpen accessSenior authorCorresponding

  The biomarker 5-chlorocytosine (5ClC) appears in the DNA of inflamed tissues. Replication of a site-specific 5ClC in a viral DNA genome results in C → T mutations, which is consistent with 5ClC acting as a thymine mimic in vivo. Direct damage of nucleic acids by immune-cell-derived hypochlorous acid is one mechanism by which 5ClC could appear in the genome. A second, nonmutually exclusive mechanism involves damage of cytosine nucleosides or nucleotides in the DNA precursor pool, with subsequent utilization of the 5ClC deoxynucleotide triphosphate as a precursor for DNA synthesis. The present work characterized the mutagenic properties of 5ClC in the nucleotide pool by exposing cells to the nucleoside 5-chloro-2′-deoxycytidine (5CldC). In both Escherichia coli and mouse embryonic fibroblasts (MEFs), 5CldC in the growth media was potently mutagenic, indicating that 5CldC enters cells and likely is erroneously incorporated into the genome from the nucleotide pool. High-resolution sequencing of DNA from MEFs derived from the gptΔ C57BL/6J mouse allowed qualitative and quantitative characterization of 5CldC-induced mutations; CG → TA transitions in 5′-GC(Y)-3′ contexts (Y = a pyrimidine) were dominant, while TA → CG transitions appeared at a much lower frequency. The high-resolution mutational spectrum of 5CldC revealed a notable similarity to the Catalogue of Somatic Mutations in Cancer mutational signatures SBS84 and SBS42, which appear in human lymphoid tumors and in occupationally induced cholangiocarcinomas, respectively. SBS84 is associated with the expression of activation-induced cytidine deaminase (AID), a cytosine deaminase associated with inflammation, as well as immunoglobulin gene diversification during antibody maturation. The similarity between the spectra of AID activation and 5CldC could be coincidental; however, the administration of 5CldC did induce some AID expression in MEFs, which have no inherent expression of its gene. In summary, this work shows that 5CldC induces a distinct pattern of mutations in cells. Moreover, that pattern resembles human mutational signatures induced by inflammatory processes, such as those triggered in certain malignancies.

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• A synthetic agent ameliorates polycystic kidney disease by promoting apoptosis of cystic cells through increased oxidative stress

  Proceedings of the National Academy of Sciences · 2024-01-19 · 9 citations

  articleOpen accessCorresponding

  Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic cause of chronic kidney disease and the fourth leading cause of end-stage kidney disease, accounting for over 50% of prevalent cases requiring renal replacement therapy. There is a pressing need for improved therapy for ADPKD. Recent insights into the pathophysiology of ADPKD revealed that cyst cells undergo metabolic changes that up-regulate aerobic glycolysis in lieu of mitochondrial respiration for energy production, a process that ostensibly fuels their increased proliferation. The present work leverages this metabolic disruption as a way to selectively target cyst cells for apoptosis. This small-molecule therapeutic strategy utilizes 11beta-dichloro, a repurposed DNA-damaging anti-tumor agent that induces apoptosis by exacerbating mitochondrial oxidative stress. Here, we demonstrate that 11beta-dichloro is effective in delaying cyst growth and its associated inflammatory and fibrotic events, thus preserving kidney function in perinatal and adult mouse models of ADPKD. In both models, the cyst cells with homozygous inactivation of Pkd1 show enhanced oxidative stress following treatment with 11beta-dichloro and undergo apoptosis. Co-administration of the antioxidant vitamin E negated the therapeutic benefit of 11beta-dichloro in vivo, supporting the conclusion that oxidative stress is a key component of the mechanism of action. As a preclinical development primer, we also synthesized and tested an 11beta-dichloro derivative that cannot directly alkylate DNA, while retaining pro-oxidant features. This derivative nonetheless maintains excellent anti-cystic properties in vivo and emerges as the lead candidate for development.

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• CCDC 2218762: Experimental Crystal Structure Determination

  The Cambridge Structural Database · 2023-02-17

  datasetOpen access

  An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  PublisherDOI

• CCDC 2218758: Experimental Crystal Structure Determination

  The Cambridge Structural Database · 2023-02-17

  datasetOpen access

  An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  PublisherDOI

Recent grants

• NIH Grant R01CA043066

  NIH · $446k · 1992

• Intra and Extra-Chromosomal Probes for Mutagenesis by Carcinogens

  NIH · $6.4M · 1998–2027

• NIH Grant R01CA086061

  NIH · $2.9M · 2012

• NIH Grant R01CA033821

  NIH · $713k · 1990

• Training Grant in Environmental Toxicology

  NIH · $18.4M · 1975–2026

Frequent coauthors

• Robert G. Croy

  Center for Environmental Health

  126 shared

• Bogdan I. Fedeles

  Massachusetts Institute of Technology

  99 shared

• James C. Delaney

  Visterra (United States)

  85 shared

• Deyu Li

  Institute of Microbiology

  50 shared

• Gerald N. Wogan

  46 shared

• Catherine L. Drennan

  Massachusetts Institute of Technology

  38 shared

• Supawadee Chawanthayatham

  Massachusetts Institute of Technology

  36 shared

• Vipender Singh

  35 shared

Education

• PhD, Biological Engineering

  Massachusetts Institute of Technology