hepacomet

HepaCometChip Enables SRP Research and Chemical Safety Testing

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A blind spot for high throughput genotoxicity assays is the inability to detect bulky lesions on DNA that have the potential to be carcinogenic. To overcome this limitation, Drs. Lizzie Ngo and Norah Owiti from the Engelward laboratory developed new methodologies for the CometChip, a high throughput comet assay developed at MIT. By incorporating hepatocytes, the platform can detect bulky lesions that are formed as a consequence of metabolic activation. Another challenge is that bulky lesions are not easily detected using the traditional comet assay, which reveals the presence of strand breaks but not bulky lesions. By incorporating inhibitors of DNA synthesis, the new assay traps repair intermediates, effectively enabling the cell to convert undetectable bulky lesions into detectable strand breaks. The assay is currently being used for a collaboration between an environmental science and engineering project and a biomedical project, where the goal is to identify novel PAH breakdown products and to test their biological impact. The new platform can also be used to screen for chemical safety and is described in a manuscript published in Nucleic Acids Research (DOI: 10.1093/nar/gkz1077). This work was featured in Technology Networks, Science Daily, the MIT News, and as an NIEHS Paper of the Month.

Dr. Amanda Armijo

Trainee Spotlight | Dr. Amanda Armijo

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Amanda Armijo, a postdoctoral fellow at MIT Professor John Essigmann’s group in the Department of Biological Engineering and Dr. James Fox’s group in the Division of Comparative Medicine, is studying the genotoxic signatures caused by environmental contaminants and how these mutations result in development of liver cancer. Specifically, her research focuses on the mutational patterns induced by the probable human carcinogen, N-nitrosodimethylamine (NDMA). NDMA is key contaminant of the Superfund site in Wilmington, MA, which for many years has contaminated the drinking water from several municipal wells.  As part of the MIT Superfund Research Program, Amanda is utilizing a high-fidelity duplex consensus sequencing (DS) method to reveal early onset genetic signatures of environmental toxicant-driven human diseases that occur later in life. Identifying these mutational processes can inform strategies for Superfund site remediation as well as clinical genetic disease early-detection, intervention and prevention.

These experiments are being performed in transgenic C57Bl/6 mice that contain a reporter gene to enable a mutational assessment and high-fidelity sequencing of the changes in the DNA triplets in the reporter gene region. To accomplish this, the transgenic mice are treated with a carcinogenic regimen of NDMA and then liver DNA is analyzed 10 weeks post-exposure (prior to development of cancerous lesions) with DS to produce high resolution mutational spectra (HRMS). DS is a highly accurate method to identify rare, unique mutations present in a heterogenous genetic milieu.  Mutational spectra patterns will also be identified in lesions that have fully developed into pathological cancer induced by NDMA. Gene-environment interactions that define inter-individual variations in sensitivity to NDMA will be identified using mutational patterns.

Amanda received her Bachelor’s degree in Microbiology, Immunology, and Molecular Genetics from UCLA. After working as a laboratory technician, she entered graduate school at UCLA in the department of Molecular and Medical Pharmacology where her work focused on the link between nucleotide metabolism and DNA replication stress responses. Her graduate work subsequently led to the preclinical development of a panel of small molecule inhibitors of deoxycytidine kinase as an anti-cancer therapeutic. Amanda successfully defended her dissertation and next attended Cornell University’s College of Veterinary Medicine, receiving a Doctor of Veterinary Medicine degree. Following completion of her DVM, Amanda completed an internship in Laboratory Animal Surgery and Medicine at Tufts University. She is happy to have found a program at MIT that combines her interests in both caring for laboratory animals and in performing important research that can positively impact human health. In her spare time, she enjoys sports, volunteering for spay/neuter clinics, cooking, and spending time with her family.

In Vitro Mutagenicity Testing

Adaptation of an Animal Mutation Model to Cell Culture Enables Rapid In Vitro Mutagenicity Testing

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There is much interest in understanding the mechanisms underlying the complex patterns displayed in mutational spectra, because these spectra will help to illuminate the molecular etiology of genetic diseases, such as cancer. The lambda gpt delta C57BL/6J mouse is an extraordinarily useful model for the probing underlying mechanisms of human cancer, and the mutational spectra of dozens of environmental carcinogens have been characterized using this transgenic animal model. Responding to the need for a high-throughput cell culture model derived from this mouse, Dr. Pennapa Thongararm from the Essigmann lab used lentiviral transformation to produce mouse embryo fibroblast cell lines. She then tested the utility of these cells for studies of the kind of DNA damage (specifically, methylation damage) that is produced by N-nitrosamines, environmental carcinogens that are the focus of MIT SRP research.

Studies by Dr. Thongaram et al., recently published in Chemical Research in Toxicology, show a clear induction of methylation damage-induced mutations, with the predominant mutation being G to A. Based on the chemistry of the DNA damage that is formed by methylating agents, the team predicted that these mutations might be coming from O6-methylguanine, which can mispair efficiently with thymine. To test this possibility, the team used a chemical inhibitor of the protein that repairs O6MeG and queried the resulting mutation pattern. They saw a clear enhancement of the original signature, providing direct evidence that O6MeG is the main driver of mutagenicity from methylating agents, and calling attention to the importance of DNA repair as a key player in suppressing methylation-induced mutations. This work opens doors to studies of methylation damage-induced mutations in vivo where ongoing collaborative work is uncovering the importance of gene-environment interactions as modulators of the risk of cancer from exposure to environmental contaminants. Publication DOI: 10.1021/acs.chemrestox.9b00444

Drs. Vandiver, Kay, and Engelward tour the Passamaquoddy Water District Treatment Facility

MIT / Passamaquoddy Tribe Engagement

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On August 2, 2019, a team from MIT SRP visited stakeholders in Maine, including A.E. Hodsdon Consulting Engineers in Waterville, ME, the group that oversees the drinking water treatment facility for the Passamaquoddy Tribe at Pleasant Point. The district is known as the Passamaquoddy Water District (PWD) and facility’s water source, Boyden Lake, has been known for years to be very challenging. The lake is small and shallow with a several residential homes on it and the treatment facility draws it water from a small impoundment area located downstream from the lake.

Drs. Kay, Engelward, and Vandiver meet with A.E. Hodsdon Engineers. From left, Mark McClusky, Jenny Kay, Bevin Engelward, Kathy Vandiver, and Al Hodsdon.

Drs. Jennifer Kay, Kathy Vandiver, and Bevin Engelward met with engineer Mark McCluskey and company president Al Hodsdon, who provided a technical overview of challenges that PWD faces in maintaining the standards for this public water supply. The facility is supervised by Hodsdon’s because the district doesn’t have a licensed operator. Seasonal changes and weather-related events produce high levels of organic material, discoloring the drinking water and raising the tribe’s concern about water purity and safety. Additionally, the PWD’s published water quality tests have exceeded the state standards for trihalomethanes (THMs) from time to time, triggering public notices that last for three months and increasing fears about water quality. THMs are commonly formed in water containing organic material that is treated with high levels of chlorination to overcome microbial risk. At our Hodsdon meeting, the MIT team pointed out that conditions that produce THMs also produce of N-nitrosodimethylamine (NDMA), one of MIT’s contaminants of concern. Our discussion with the Hodsdon engineers led the MIT team to conclude that a follow-up trip to Maine with the goal of testing for NDMA at several locations in the PWD district would be supported and welcomed.

Drs. Vandiver, Kay, and Engelward tour the Passamaquoddy Water District Treatment FacilityIn addition to visiting the engineers in Waterville, the MIT SRP team also met with the newly elected Vice Chief of the Passamaquoddy Tribe at Pleasant Point, Maggie Dana. At this meeting, Drs. Jennifer Kay, Kathy Vandiver, Bevin Engelward, and John Essigmann met with Brownfields Coordinator Dale Mitchell and members of the Sipayik Environmental Department, including Director Marvin Cling, Water Quality Manager Billy Longfellow, and Ecology Coordinator Chris Johnson. Overall, tribal members are still quite concerned about ongoing issues with the municipal PWD water supply, in particular the frequent water discoloration and PWD notices of THMs exceedances. The Passamaquoddy expressed a continuing interest in collaborations with MIT scientists in water quality studies.

The MIT SRP is well-positioned to assist with water quality testing as members of the MIT team have previously partnered with Sipayik Environmental Dept. members (named above) in a citizen science project testing for metals, including lead and arsenic in PWD water and well water used by the Passamaquoddy tribe. This successful research collaboration between MIT and the Passamaquoddy Environmental Dept. was both a capacity-building and trust-building experience. Tribal households received back their individual results for lead and arsenic levels in their drinking water with recommendations for how to reduce their exposures. This study laid the groundwork for a future partnership with our Passamaquoddy colleagues to address additional water quality concerns such as NDMA.

MIT SRP team concluded the tribal visit with a separate meeting with Passamaquoddy Brownfields Coordinator Dale Mitchell to learn more about the Meddybemps Superfund site. This site harbors a wealth of native artifacts dating back more than 8,000 years. The site is located on Meddybemps Lake, a major native trading route and an important Passamaquoddy ancestral home.  Today’s tribal elders have named this place “Ntolonapemk” — “My Relatives’ Place.” The tribe feels a great spiritual connection to this place and to their tribal ancestors and they are hoping to acquire this land in the near future. The MIT team expressed an interest in supporting the Passamaquoddy with regard to the assessment of the environmental health risks associated with the Meddybemps Superfund site.

data management analysis

The Data Management and Analysis Core Takes Off at MIT

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With support from the NIEHS, MIT SRP is developing new infrastructure that enables data to be combined in new ways and that ensures FAIR practices. An exciting development is the ability to upload metadata in real time for wide ranging data sets, including environmental as well as biological data. The new Data Management Core will build off of the open access SEEK platform to create a system where researchers from vastly different fields can share and interpret each other’s metadata, facilitating collaborations that are key to SRP success.

Prof. Hurt, Prof. Timothy Swager, and Bevin Engelward

Brown University SRP Director Prof. Robert Hurt Presented at Friday Forum Seminar Series

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On February 21, 2020, Prof. Robert Hurt (Program Director and Project 4 PI for the Brown University SRP) visited MIT to give a lecture as part of the Friday Forum seminar series. This lecture was co-sponsored by the MIT SRP and Center for Environmental Health Sciences (CEHS). Prof. Hurt provided an overview of the Brown SRP and discussed the program’s research on graphene-based nanomaterials. In particular, Prof. Hurt’s team is developing nanomaterials for advanced barrier technologies to prevent exposure to toxic contaminants. During his talk, he emphasized the cross disciplinary work of the Brown SRP. As one example, Prof. Hurt’s engineering team works closely with Prof. Agnes Kane’s team of toxicological researchers in order to evaluate the risks associated with exposure to relevant nanomaterials. Together, these complementary engineering and biological research projects will lead to development of safer, more effective barriers against environmental toxicants. During his visit, Prof. Hurt (center) discussed graphene-based materials and their potential uses with Prof. Timothy Swager (MIT SRP Projects 1 and 2; left) and Bevin Engelward (MIT SRP Director; right).

Carbon Nanotube-Based Sensor

Carbon Nanotube-Based Sensor Detects Nitrosamines in Air

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A collaboration between environmental science and engineering researchers and biomedical researchers from the MIT SRP has led to the development of a carbon nanotube (CNT) based sensor that enables detection of nitrosamines in air. The sensor was developed by Dr. Maggie He of Prof. Timothy Swager’s laboratory in collaboration with Prof. John Essigmann and Dr. Robert Croy. The approach utilizes functionalized CNTs that can bind nitrosamines spanning across gold electrodes. Specific binding of nitrosamines to the CNTs produces a change in current proportional to the level of chemical in the air. These inexpensive sensors present opportunities for improved remediation efforts at the Olin Chemical Superfund site in Wilmington MA, and they were featured in an article by Chemical & Engineering News, as an NIEHS Paper of the Month, and in an NIEHS SRP Research Brief article and podcast.

NewGen Protocols

NextGen Protocols

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The MIT SRP Research Translation Core is pleased to share NextGen Protocols. Detailed experimental protocols used in SRP research are being shared so that the exact methods of each experiment can be linked to data sets produced by those experiments. The MIT SRP invites trainees from all SRP centers to use the website. The protocols on NextGen Protocols are intended to be fully descriptive of the experimental process to make it easier to reproduce results. This platform allows the researcher to explain every step they take with no limit on length. A key advantage to posting a NextGen Protocol is that video clips can be shared. Seeing how tricky steps are done is a great way to share methods. By facilitating reproducibility and allowing researchers to link their data to the protocol that produced it, NextGen Protocols aims to clarify and streamline the process of sharing complete methods widely.
community meeting

MIT SRP in the News

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MIT Homepage News Spotlight: Work from MIT SRP trainees Hélène Angot and Nicholas Hoffman was featured on the MIT Homepage. The article discussed their research with Prof. Noelle Selin (Project 2), studying the atmospheric transport and transformation of mercury and the impacts of mercury bioaccumulation in fish.

MIT SRP Citizen Science in the News: Abigail Harvey and Tchelet Segev, two Master’s students trained by Dr. Kathy Vandiver and supported by Harry Hemond, John Essigmann and Robert Croy, completed their Citizen Science Project focused on drinking water quality for the Passamaquoddy Tribe located in Maine. This citizen science project was initiated by the MIT Center for Environmental Health Sciences (CEHS) and supported by both the CEHS and the MIT Superfund Research Program. Tribe members expressed concern about their drinking water. Students learned how to design the study, and how to engage effectively with community members. Importantly, with coaching, the students led Community Meetings where the project and results were shared in a bidirectional fashion. Under the guidance of K. Vandiver, the students successfully engaged with ~20% of households (representing three towns and including Passamaquoddy Tribe members from Pleasant Point). Sampling methods were optimized and reported back to individuals and the Maine Environmental Department. The impact from this study included teaching people how to flush their water to reduce lead exposure. In addition, several homes were notified that their arsenic levels exceeded national standards. This opened the doors for those individuals to obtain safer water from other sources. This work served as an excellent pilot study in support of future Citizen Science projects directly related to the toxicants of study by the MIT Superfund Research Program. The study and its impact were described in several publications, including two Quoddy Tides Newspaper articles, and the NIEHS PEPH Newsletter.

Dr. John Essigmann and Dr. Kathleen Vandiver travel to the Loring Air Force Base Superfund site

Visit to Loring AFB Superfund Site

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In August 2018, MIT SRP Program Director Prof. Bevin Engelward, Co-Director Prof. John Essigmann, and Community Engagement Core Leader Dr. Kathleen Vandiver traveled to the Loring Air Force Base Superfund site.

The former Loring AFB is contaminated with a variety of harmful chemicals, including PCBs, PAHs, and PFAS at different sites around the property. Following extensive remediation, the land was divided into parcels, one of which was given to the Aroostook Band of Micmacs. However, subsequent testing revealed that contamination remains at unsafe levels for food gathering or residences. There is also an advisory that fish should not be eaten due to dangerously high contamination by PCBs, and volatile organic chemicals continue to intrude into buildings left behind.

The MIT SRP team met with Peter Forbes of the US Air Force and Fred Corey’s team at the Micmac Environmental Lab to discuss the current status of the site and to explore the site on foot. The team gained improved understanding of the site’s geography and locations of contaminants, including in remediated areas. Tribal environmental concerns were discussed with Mr. Corey, and the team continues to work with both Mr. Corey and Mr. Forbes to develop specific plans for MIT-driven research. The team plans to return to collect soil, sediment and water samples to test for the presence of carcinogens, including N-nitrosodimethylamine and polycyclic aromatic hydrocarbons, the focus of the MIT SRP.