“People have been using FOXR2 activation as a clinical diagnostic for CNS neuroblastoma,” said corresponding author Jason Cheng-Hsuan Chiang, MD, PhD, St. Jude Department of Pathology. “But we unexpectedly saw it in a patient’s recurrent non-neuroblastoma tumor, which motivated us to look into other brain tumors.”

The researchers searched for and found FOXR2 activation using data from the St. Jude Cloud, which houses whole genome, whole exome and RNA sequencing data from St. Jude patients. In total, they identified 42 tumors with activated FOXR2 in 41 patients. Only 11 of the tumors were the expected CNS neuroblastoma. The other 31 were a mix of high-grade gliomas and other embryonal and rare tumors, indicating a large, previously undiscovered category of disease with implications for diagnosis, prognosis and treatment.

“When we looked at the clinical outcomes of the different types of tumors with FOXR2 activation, there was a pretty stark difference,” said co-first author Emily Hanzlik, MD, St. Jude Department of Pediatric Medicine. “The CNS neuroblastomas had an exceptionally good outcome when they were treated with multimodal therapy, whereas the other types of tumors in the cohort, the high-grade gliomas and the pineoblastomas, had pretty dismal outcomes.”

Those differences indicate that physicians should not use FOXR2 activation as an exclusive marker of CNS neuroblastoma since it can occur in other tumor types. “Hopefully, our findings can help guide patients to the most appropriate clinical care,” Chiang said.

Finding undetected mechanisms of FOXR2 activation in multiple brain tumor types

The underlying mechanisms of FOXR2 activation has gone unnoticed in brain tumors due to the difficulty in identifying them using standard molecular diagnostics. Still, the St. Jude scientists closely examined the clinical genomic data from the St. Jude Cloud to discover and better describe these hard-to-detect alterations.

“Now that we described these genomic events, hopefully, others will be able to detect them in their patients as well,” said co-first author Alexa Siskar, PhD, St. Jude Department of Pathology, who analyzed the genomic data.

“Our study highlights the importance of combining every piece of information we have for classifying a patient’s tumors, including molecular findings like DNA and RNA sequencing, histology and imaging,” Chiang added. “Only with a holistic view can we correctly understand a specific brain tumor and choose the best treatment approach for that patient.”

The findings were published in the Journal of Applied Microbiology on April 15, 2025.

The team identified 455 species of microorganisms wielding 64 different biochemical pathways to degrade pollutants and 1,171 genes to process heavy metals. This suggests the potential of a cheaper, more sustainable, and less disruptive method for cleaning contaminated waterways than the current oft-used dredging operations.

The researchers also discovered 2,300 novel genetic sequences that could enable microbes to produce potentially valuable biochemical compounds for medicine, industry, or environmental applications.

“We found what amounts to nature’s own toxic cleanup manual, but with a crucial warning,” said Hénaff, who sits in NYU Tandon’s Technology, Culture and Society Department and is a member of Tandon’s Center for Urban Science + Progress. “These microbes have stories to tell that go beyond scientific data.”

To communicate these stories effectively, Hénaff and colleagues created CHANNEL, an immersive installation at BioBAT Art Space in Brooklyn, New York featuring sculpture, prints, sound, and projections alongside over 300 gallons of native Gowanus sediment and water that has been growing over the last 9 months. The Living Interfaces Lab, Hénaff’s research group, uses methods from sciences and arts to address pressing urban issues.

“While more research is needed to understand how to cooperate with these organisms effectively, the discovery of such genetic tools for pollution cleanup may offer valuable lessons for environmental restoration worldwide,” Hénaff said. “I consider artistic research to be a key component in not just illustrating but also informing our scientific research.” The work is on view at the exhibit’s closing event on April 18, 2025.

The team discovered genes for resistance to eight different classes of antibiotics in the canal microbes, with some coming from human gut bacteria that enter the canal during Combined Sewer Overflows — when heavy rainfall causes stormwater and untreated sewage to discharge directly into waterways. Other resistance genes were found in native aquatic species.

“The long-term coexistence of microbial communities from sewage and the natural canal environment is expected to enhance the rates of horizontal transfer of a wide array of genetic elements, and as such merits our attention for public health monitoring and surveillance as environmental ‘superbug’ reservoirs,” said Sergios-Orestis Kolokotronis, a study co-author and assistant professor of epidemiology and infectious diseases at SUNY Downstate Health Sciences University.

Despite these concerns, the study also reveals promising potential benefits. While the pollutant-degrading microbes in the canal can break down contaminants, their natural processes are too slow for practical cleanup. Understanding their genetic adaptations could help scientists develop faster methods, either by isolating specific microbes for treatment or enhancing their abilities.

Some classes of contaminants such as heavy metals are also valuable materials for industry, and bioremediation methods could be adapted to resource recovery for re-use, not just removal.

To make its discoveries, the team collected samples from 14 locations along the canal’s 1.8-mile length, gathering both surface sediment and deep core samples reaching 11.5 feet below the canal floor. They found microbes capable of breaking down many historical pollutants, including petroleum products, PCBs, and industrial solvents.

The findings come as the Environmental Protection Agency continues its $1.5 billion dredging and capping operation at the canal, removing contaminated sediment and sealing remaining pollution under clean material.

The team’s current study builds on prior research spanning a decade to understand the Gowanus Canal microbiome. The project began in 2014 when the current study’s co-authors Ian Quate of Fruit Studio and Matthew Seibert of the University of Virginia led the first sediment sampling, processing samples at community bio lab Genspace with study co-author Ellen Jorgensen of Biotech without Borders.

The DNA was sequenced in the lab of study co-author Christopher Mason — WorldQuant Professor of Genomics and Computational Biomedicine at Weill Cornell Medicine — as part of the Pathomap Project, now expanded to cities around the world in the metagenomics of subways and urban biomes (MetaSUB) project.

“The hardy microbial organisms of the Gowanus Canal have a unique genetic catalog of survival, which provides a roadmap for adaptation and directed evolution that we can use in polluted sites around the world,” said Mason, who serves as co-founder and Director of the MetaSUB Consortium.

Later, lead author Hénaff’s team collected more samples through the BKBioReactor project while study co-author Kolokotronisgathered core samples. Bioinformatic approaches implemented by study co-authors Chandrima Bhattacharya of Weill Cornell Medicine and Rupobrata Panja of Rutgers University allowed the team to identify microbes breaking down industrial pollutants in the canal’s thick sediment.

This research was supported by funding from WorldQuant Foundation, the Pershing Square Foundation, National Aeronautics and Space Administration, National Institutes of Health, National Science Foundation and NYU Tandon.

Urinary incontinence — the loss of bladder control — is a common condition, especially in older adults. Previous studies have stated that it can affect between 38% and 60% of women. The researchers aimed to find out whether urinary incontinence was linked to a decline in physical activity, which can lead to a host of health issues, including greater risk for cardiovascular disease.

In the study, the researchers — led by Lisa VanWiel, assistant professor at the University of Wisconsin-La Crosse who in April earned her doctorate in health and human physiology from Iowa — analyzed medical records over two years from more than 20,000 female patients in the Hartford Healthcare system in Connecticut. Of those patients, 5.4% reported through a questionnaire to have urinary incontinence. All patients were asked to rate their level of physical activity in the questionnaire.

The researchers found that the respondents with urinary incontinence did not report engaging in less physical activity than those who did not have the condition. But the team did find an association between patients with urinary incontinence and cardiovascular disease risk factors or events, such as dyslipidemia, type 2 diabetes, and stroke.

“There is an association between incontinence and cardiovascular disease (CVD) risk,” the study authors write. “Women should be screened for incontinence regularly as it may contribute to CVD risk, and women with CVD risk factors should be screened for undiagnosed incontinence.”

VanWiel is the study’s corresponding author. Co-authors from Iowa are Kara Whitaker, associate professor in the Department of Health and Human Physiology, who is VanWiel’s mentor; and Lucas Carr, associate professor in the Department of Health and Human Physiology. Other co-authors are Dale Bond, Yin Wu, Elena Tunitsky-Bitton, Paul Tulikangas, and Adam Steinberg, all from Hartford Hospital.

The metals have previously been shown to damage the health of pollinators, which ingest them in nectar as they feed, leading to reduced population sizes and death. Even low nectar metal levels can have long-term effects, by affecting bees’ learning and memory — which impacts their foraging ability.

Researchers have found that common plants including white clover and bindweed, which are vital forage for pollinators in cities, can accumulate arsenic, cadmium, chromium and lead from contaminated soils.

Metal contamination is an issue in the soils of cities worldwide, with the level of contamination usually increasing with the age of a city. The metals come from a huge range of sources including cement dust and mining.

The researchers say soils in cities should be tested for metals before sowing wildflowers and if necessary, polluted areas should be cleaned up before new wildflower habitats are established.

The study highlights the importance of growing the right species of wildflowers to suit the soil conditions.

Reducing the risk of metal exposure is critical for the success of urban pollinator conservation schemes. The researchers say it is important to manage wildflower species that self-seed on contaminated urban land, for example by frequent mowing to limit flowering — which reduces the transfer of metals from the soil to the bees.

The results are published today in the journal Ecology and Evolution.

Dr Sarah Scott in the University of Cambridge’s Department of Zoology and first author of the report, said: “It’s really important to have wildflowers as a food source for the bees, and our results should not discourage people from planting wildflowers in towns and cities.

“We hope this study will raise awareness that soil health is also important for bee health. Before planting wildflowers in urban areas to attract bees and other pollinators, it’s important to consider the history of the land and what might be in the soil — and if necessary find out whether there’s a local soil testing and cleanup service available first.”

The study was carried out in the post-industrial US city of Cleveland, Ohio, which has over 33,700 vacant lots left as people have moved away from the area. In the past, iron and steel production, oil refining and car manufacturing went on there. But any land that was previously the site of human activity may be contaminated with traces of metals.

To get their results, the researchers extracted nectar from a range of self-seeded flowering plants that commonly attract pollinating insects, found growing on disused land across the city. They tested this for the presence of arsenic, cadmium, chromium and lead. Lead was consistently found at the highest concentrations, reflecting the state of the soils in the city.

The researchers found that different species of plant accumulate different amounts, and types, of the metals. Overall, the bright blue-flowered chicory plant (Cichorium intybus) accumulated the largest total metal concentration, followed by white clover (Trifolium repens), wild carrot (Daucus carota) and bindweed (Convolvulus arvensis). These plants are all vital forage for pollinators in cities — including cities in the UK — providing a consistent supply of nectar across locations and seasons.

There is growing evidence that wild pollinator populations have dropped by over 50% in the last 50 years, caused primarily by changes in land use and management across the globe. Climate change and pesticide use also play a role; overall the primary cause of decline is the loss of flower-rich habitat.

Pollinators play a vital role in food production: many plants, including apple and tomato, require pollination in order to develop fruit. Natural ‘pollination services’ are estimated to add billions of dollars to global crop productivity.

Scott said: “Climate change feels so overwhelming, but simply planting flowers in certain areas can help towards conserving pollinators, which is a realistic way for people to make a positive impact on the environment.”