SRP

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SEEK ID: https://nextseek-dev.mit.edu/investigations/6

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Created: 21st Jan 2026 at 15:07

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Studies (12+1)
Assays (61+5)
SOPs (22)
Publications (11)
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Demo Demo

Projects: Published Data

Institutions: BMC-BioMicro Center (MIT)

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Showing 5 out of a possible 12 Studies Advanced Studies list for this Investigation with search and filtering

DNA adduct and mutational profiles reveal a threshold of cellular defenses against N-nitrosodimethylamine administered to mice in drinking water

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Nina Gubina, Lindsay B. Volk, Anna Dormitzer, Emily Michelsen, Lee J. Pribyl, Joshua J. Corrigan, Esha Dalvie, Amanda L. Armijo, Nicolette A. Bugher, Kayla Shonvisky, Monét Norales, Desiree L. Plata, Bevin P. Engelward, Robert G. Croy, John M. Essigmann, Bogdan I. Fedeles

DOI:

Abstract: N-Nitrosodimethylamine (NDMA) is an animal and probable human carcinogen. Here DNA adduct and high-resolution mutational spectra were correlated following administration of ...

Submitter: Demo Demo

Investigation: SRP

Assays: All Metadata, Chemical Challenge - Metadata, DNA Extraction - Metadata, ELISA - Data Linked, GPT Assay - Data Linked, Library Prep - Metadata, Mass Spectrometry - Data Linked, Mutational Spectra Analysis - Data Linked, PCR - Data Linked, RNA Extraction - Metadata, RaDR - Data Linked, Short Read Sequencing - Data Linked, Tissue Collection - Metadata

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Created: 22nd Jan 2026 at 20:16, Last updated: 25th Aug 2026 at 14:14

Youth Dictates Susceptibility to DNA Damage-Induced Genotoxicity, Mutagenesis, and Tumorigenesis from N-Nitrosamine Exposure in Mice

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The data / metadata will be available ** online** at the time of paper acceptance. If you would like access prior to acceptance, please reach out to Lindsay Volk: (lvolk@mit.edu)

Submitter: Demo Demo

Investigation: SRP

Assays: No Assays

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Created: 22nd Jan 2026 at 20:16

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

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DOI: https://www.biorxiv.org/content/10.1101/2025.10.01.679856v1

Submitter: Demo Demo

Investigation: SRP

Assays: No Assays

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Created: 22nd Jan 2026 at 20:16

Reversible Electrochemical Sensor for NDMA: Leveraging Molecularly Imprinted Polymers for Enhanced Sensitivity and Selectivity

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Zhewen Guo, Haosheng Feng, Timothy Swager

DOI: https://pubs.acs.org/doi/10.1021/acssensors.4c02462

Abstract: Herein, we present the development and evaluation of a molecularly imprinted polymer (MIP) sensor for the sensitive and selective detection of N-nitrosodimethylamine (NDMA) in aqueous environments. MIP coatings over electrochemically active electrodes enable NDMA detection with a notably low detection limit of 1.16 ppb. Our findings demonstrate that the ...

Submitter: Demo Demo

Investigation: SRP

Assays: Atomic Force Microscopy - Data Linked, Chemical Simulations - Data Linked, Chemical Synthesis - Metadata, Electrochemical Sensor Testing - Data Linked, Sensor Creation - Metadata

Snapshots: No snapshots

Created: 21st Jan 2026 at 15:08

Colorimetric Detection of Aqueous N-Nitrosodimethylamine via Photonitrosation of a Naphtholsulfonate Indicator

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Auto-created study: Colorimetric Detection of Aqueous N-Nitrosodimethylamine via Photonitrosation of a Naphtholsulfonate Indicator

Submitter: Demo Demo

Investigation: SRP

Assays: Chemical Synthesis - Metadata, Imaging - Data Linked, Nuclear Magnetic Resonance - Data Linked, Nuclear Magnetic Resonance Analysis - Data Linked, Single-crystal X-ray Crystallography - Data Linked, UV-Vis Spectroscopy - Data Linked, UV-Vis Spectroscopy Analysis - Data Linked

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Created: 21st Jan 2026 at 15:08

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Mass Spectrometry Processing – Data Linked

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Submitter: Demo Demo

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: SRP

Study: Excision of mutagenic replication-blocking lesi...

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

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Created: 21st Jan 2026 at 15:12

Mass Spectrometry – Data Linked

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Submitter: Demo Demo

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: SRP

Study: Excision of mutagenic replication-blocking lesi...

Organisms: No organisms

SOPs: No SOPs

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Created: 21st Jan 2026 at 15:12

Tissue Imaging – Metadata

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Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: SRP

Study: Excision of mutagenic replication-blocking lesi...

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

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Created: 21st Jan 2026 at 15:12

RaDR Image Machine Learning Analysis – Data Attached

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Submitter: Demo Demo

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: SRP

Study: Excision of mutagenic replication-blocking lesi...

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

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Created: 21st Jan 2026 at 15:12

Tissue Lysis – Metadata

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Submitter: Demo Demo

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: SRP

Study: Excision of mutagenic replication-blocking lesi...

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

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Created: 21st Jan 2026 at 15:12

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P.ESS-251028-V1_NG_8-GEX.docx

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Submitter: Demo Demo

Investigations: SRP

Studies: DNA adduct and mutational profiles reveal a thr...

Assays: PCR - Data Linked, RNA Extraction - Metadata

Created: 23rd Jan 2026 at 18:27, Last updated: 23rd Jan 2026 at 18:27

P.ESS-251028-V1_NG_3-DNA_Adducts.docx

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Submitter: Demo Demo

Investigations: SRP

Studies: DNA adduct and mutational profiles reveal a thr...

Assays: Mass Spectrometry - Data Linked

Created: 23rd Jan 2026 at 18:14, Last updated: 23rd Jan 2026 at 18:14

P.ESS-251028-V1_NG_6-DuplexDNA.docx

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Submitter: Demo Demo

Investigations: SRP

Studies: DNA adduct and mutational profiles reveal a thr...

Assays: DNA Extraction - Metadata, Library Prep - Metadata, Mutational Spectra Analysis - Data Linked, Short Read Sequencing - Data Linked

Created: 23rd Jan 2026 at 18:14, Last updated: 23rd Jan 2026 at 18:14

P.ESS-251028-V1_NG_9-ELISA.docx

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Submitter: Demo Demo

Investigations: SRP

Studies: DNA adduct and mutational profiles reveal a thr...

Assays: ELISA - Data Linked

Created: 23rd Jan 2026 at 18:13, Last updated: 23rd Jan 2026 at 18:13

P.ESS-251028-V1_NG_2-NDMA.docx

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Submitter: Demo Demo

Investigations: SRP

Studies: DNA adduct and mutational profiles reveal a thr...

Assays: Chemical Challenge - Metadata

Created: 23rd Jan 2026 at 18:10, Last updated: 23rd Jan 2026 at 18:10

View all 22 SOPs

Showing 5 out of a possible 11 Publications Advanced Publications list for this Investigation with search and filtering

DNA adduct and mutational profiles reveal a threshold of cellular defenses against N-nitrosodimethylamine administered to mice in drinking water.

Published Data

Abstract (Expand)

N-Nitrosodimethylamine (NDMA) is classified as an animal and probable human carcinogen. Murine liver DNA adducts, mutations, O (6)-methylguanine DNA methyltransferase (MGMT), and CYP2E1 were evaluated … following chronic administration of NDMA in drinking water. In a dose-escalation study, 7-methylguanine (m7G) increased linearly with NDMA dose. O (6)-Methylguanine (m6G) remained near background for NDMA doses up to approximately 1 ppm, beyond which its level, and corresponding mutations, rose steeply. An extended study was done with 5 ppm NDMA, in which adducts were measured at 3 and 10 weeks and mutations at 10 weeks. We found that both sexes experienced elevated levels of point mutations closely tracking with the levels of m6G, which emerged as the dominant mutagenic adduct under chronic dosing with NDMA. Homologous recombination-mediated chromosomal rearrangements, however, did not increase over background. Mutational analysis over 96 trinucleotide contexts revealed predominantly GC-->AT mutations in 5'-purine-G-3' contexts in a pattern matching human COSMIC cancer mutational signature SBS11, with secondary features resembling SBS119 (AT-->GC). Moreover, we identified the m6G level ( approximately 2000 adducts/diploid genome) above which its dedicated repair protein, MGMT, became saturated. The coordinated application of DNA adduct, mutational, and biochemical analyses provides a new approach for studying mechanisms of carcinogenesis, with relevance to early cancer detection and cancer management.

Authors: N. E. Gubina, L. B. Volk, A. F. Dormitzer, E. M. Michelsen, L. J. Pribyl, J. J. Corrigan, E. D. Dalvie, A. L. Armijo, M. Norales, N. A. Bugher, K. M. Schonvisky, D. L. Plata, B. P. Engelward, R. G. Croy, J. M. Essigmann, B. I. Fedeles

Date Published: 15th Jul 2026

Publication Type: Journal Article

PubMed ID: 42453099

DOI: 10.1093/narmme/ugag035

Citation: NAR Mol Med. 2026 Jun 26;3(3):ugag035. doi: 10.1093/narmme/ugag035. eCollection 2026 Jul.

Created: 25th Aug 2026 at 18:49

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

Published Data

Abstract (Expand)

N-Nitrosodimethylamine (NDMA), a probable human carcinogen, induces toxic and mutagenic O (6)-methylguanine lesions that are repaired by the O (6)-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.

Authors: L. J. Pribyl, J. E. Kay, J. J. Corrigan, L. B. Volk, M. Norales, N. A. Owiti, E. A. Kowal, I. N. Kohale, I. S. Nazari, M. R. Swanson, A. C. Moise, D. Ma, S. S. Levine, E. Michelsen, R. G. Croy, T. Ragan, D. K. Torous, S. L. Avlasevich, S. D. Dertinger, S. E. Carrasco, L. D. Samson, J. M. Essigmann, F. M. White, B. P. Engelward

Date Published: 3rd Oct 2025

Publication Type: Journal Article

PubMed ID: 41256671

DOI: 10.1101/2025.10.01.679856

Citation: bioRxiv [Preprint]. 2025 Oct 3:2025.10.01.679856. doi: 10.1101/2025.10.01.679856.

Created: 25th Aug 2026 at 18:54

Reversible Electrochemical Sensor for NDMA: Leveraging Molecularly Imprinted Polymers for Enhanced Sensitivity and Selectivity.

Published Data

Abstract (Expand)

Herein, we present the development and evaluation of a molecularly imprinted polymer (MIP) sensor for the sensitive and selective detection of N-nitrosodimethylamine (NDMA) in aqueous environments. MIP … coatings over electrochemically active electrodes enable NDMA detection with a notably low detection limit of 1.16 ppb. Our findings demonstrate that the dual-monomer system employed in the MIP fabrication enhances both the selectivity and sensitivity toward NDMA. Additionally, the reversibility of the sensor was confirmed via a chronoamperometry regeneration process. Furthermore, the sensor's robustness was demonstrated across various water samples, as well as on different electrode materials, highlighting its potential for practical and reliable water quality monitoring applications.

Authors: Z. Guo, H. Feng, T. M. Swager

Date Published: 28th Feb 2025

Publication Type: Journal Article

PubMed ID: 39882871

DOI: 10.1021/acssensors.4c02462

Citation: ACS Sens. 2025 Feb 28;10(2):881-885. doi: 10.1021/acssensors.4c02462. Epub 2025 Jan 30.

Created: 25th Aug 2026 at 18:55

Colorimetric Detection of Aqueous N-Nitrosodimethylamine via Photonitrosation of a Naphtholsulfonate Indicator.

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Abstract (Expand)

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 Mossbauer 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.

Authors: J. C. Beard, C. H. Wang, A. Sridharan, R. G. Croy, J. M. Essigmann, T. M. Swager

Date Published: 27th Sep 2024

Publication Type: Journal Article

PubMed ID: 39167159

DOI: 10.1021/acssensors.4c00927

Citation: ACS Sens. 2024 Sep 27;9(9):4655-4661. doi: 10.1021/acssensors.4c00927. Epub 2024 Aug 21.

Created: 25th Aug 2026 at 18:48

Optical Detection of Interleukin-6 Using Liquid Janus Emulsions Using Hyperthermophilic Affinity Proteins.

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Abstract (Expand)

When equal volumes of two immiscible liquids are mixed (e.g., a hydrocarbon and a fluorocarbon), Janus droplets can form in an aqueous solution. In a gravity-aligned Janus droplet, the boundary between … the two phases is flat and thus optically transparent when viewed from above. When tipped due to interactions with an analyte (i.e., agglutination), the resulting change in refraction and reflection yields an optical signal that can be detected and quantified. This study reports the detection and quantitation of interleukin-6 (IL-6) using emulsions functionalized at the hydrocarbon:aqueous interface with engineered proteins that bind IL-6 at high affinity and specificity. Hyperthermophilic affinity proteins (rcSso7d) are derived from thermophiles, giving them excellent thermal stability. Two rcSso7d affinity protein variants were synthesized with a noncanonical azide-functionalized amino acid to enable click chemistry to novel polymeric anchors embedded in the hydrocarbon phase. The two binding proteins recognize different epitopes, enabling the detection of both monomeric and dimeric IL-6 via agglutination. It is noteworthy that the rsSso7d protein variants, in addition to having superior thermal stability and facile recombinant synthesis in E. coli, show superior performance when compared to commercial antibodies for IL-6.

Authors: M. Chen, E. I. Corless, B. P. Engelward, T. M. Swager

Date Published: 3rd Sep 2024

Publication Type: Journal Article

PubMed ID: 39246480

DOI: 10.1021/acsomega.4c03959

Citation: ACS Omega. 2024 Aug 22;9(35):37076-37085. doi: 10.1021/acsomega.4c03959. eCollection 2024 Sep 3.

Created: 25th Aug 2026 at 18:53

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