Previous studies have identified a link between air pollution and the risk of specific mental disorders, including depression and anxiety, but this study looked at changes in mental health that span all forms of disorder and psychological distress associated with exposure to traffic-related air pollutants.

The findings, which will appear April 28 in JAMA Network Open, reveal that the greater an individual’s exposure to nitrogen oxides across childhood and adolescence, the more likely they are to show any signs of mental illness at the transition to adulthood, at age 18, when most symptoms of mental illness have emerged or begin to emerge.

The link between air pollution exposure and young adult mental illness symptoms is modest, according to the study’s first-author Aaron Reuben, a graduate student in clinical psychology at Duke University. But “because harmful exposures are so widespread around the world, outdoor air pollutants could be a significant contributor to the global burden of psychiatric disease,” he said.

The World Health Organization (WHO) currently estimates that 9 out of 10 people worldwide are exposed to high levels of outdoor air pollutants, which are emitted during fossil fuel combustion in cars, trucks, and powerplants, and by many manufacturing, waste-disposal, and industrial processes.

In this study, air pollution, a neurotoxicant, was found to be a weaker risk factor for mental illness than other better-known risks, such as family history of mental illness, but was of equal strength to other neurotoxicants known to harm mental health, particularly childhood exposure to lead.

In a previous study in the same cohort, Helen Fisher of King’s College London’s Institute of Psychiatry, Psychology & Neuroscience, and coauthor and principal investigator for this study, linked childhood air pollution exposure to the risk of psychotic experiences in young adulthood, raising concern that air pollutants may exacerbate risk for psychosis later in life.

When combined with studies showing increased hospital admissions for many psychiatric illnesses during “poor” air quality days in countries like China and India, the current study builds on past findings to reveal that “air pollution is likely a non-specific risk factor for mental illness writ large,” said Fisher, who noted that exacerbations of mental illness risk may show up differently in different children.

The subjects of this study are a cohort of 2,000 twins born in England and Wales in 1994-1995 and followed to young adulthood. They have regularly participated in physical and mental health evaluations and have provided information about the larger communities in which they live.

Researchers measured exposure to air pollutants — particularly nitrogen oxides (NOx), a regulated gaseous pollutant, and fine particulate matter (PM2.5), a regulated aerosol pollutant with suspended particles below 2.5 microns in diameter — by modeling air quality around study member’s homes at ages 10 and 18 years using high-quality air dispersion models and data provided by the UK National Atmospheric Emissions Inventory and the Imperial College’s UK road-traffic emissions inventory. Twenty-two percent of the study members were found to have had exposure to NOx that exceeded WHO guidelines, and 84% had exposure to PM2.5 that exceeded guidelines.

The research team, based at Duke and King’s IoPPN, also assessed participant mental health at age 18. Symptoms associated with ten different psychiatric disorders — dependence on alcohol, cannabis, or tobacco; conduct disorder and attention-deficit/hyperactivity disorder; major depression, generalized anxiety disorder, post-traumatic stress disorder, and eating disorder; and thought disorder symptoms related to psychosis — were used to calculate a single measure of mental health, called the psychopathology factor, or “p-factor” for short.

The higher an individual’s p-factor score, the greater the number and severity of psychiatric symptoms identified. Individuals can also differ on their mental health across sub-domains of psychopathology, which group together symptoms of distress or dysfunction that are manifested in outwardly visible ways (externalizing problems, like conduct disorder), experienced largely internally (internalizing problems, like anxiety), and via delusions or hallucinations (thought disorder symptoms). Air pollution effects on mental health were observed across these subdomains of psychopathology, with the strongest links to thought disorder symptoms.

Unique to this study, the researchers also assessed characteristics of children’s neighborhoods to account for disadvantageous neighborhood conditions that associate with higher air pollution levels and greater risk of mental illness, including socioeconomic deprivation, physical dilapidation, social disconnection, and dangerousness. While air pollution levels were greater in neighborhoods with worse economic, physical, and social conditions, adjusting the study results for neighborhood characteristics did not alter the results, nor did adjustment for individual and family factors, such as childhood emotional and behavioral problems or family socioeconomic status and history of mental illness.

“We have confirmed the identification of what is essentially a novel risk factor for most major forms of mental illness,” said Reuben, “one that is modifiable and that we can intervene on at the level of whole communities, cities, and or even countries.”

In the future, the study team is interested in learning more about the biological mechanisms that link early life air pollution exposure to greater risk for mental illness at the transition to adulthood. Previous evidence suggests that air pollutant exposures can lead to inflammation in the brain, which may lead to difficulty regulating thoughts and emotions.

While the findings are most relevant to high-income countries with only moderate levels of outdoor air pollutants, like the US and the UK, there are also implications for low-income, developing countries with higher air pollution exposures, like China and India. “We don’t know what the mental health consequences are of very high air pollution exposures, but that is an important empirical question we are investigating further,” said Fisher.

Support for the study came from the UK Medical Research Council (MRC) [grant G1002190]; the US National Institute of Child Health and Human Development [grant HD077482]; the US National Institute of Environmental Health Science [grant F31ES029358]; Google; the Jacobs Foundation; a joint Natural Environment Research Council, UK MRC and Chief Scientist Office grant [NE/P010687/1]; and the King’s Together Multi and Interdisciplinary Research Scheme (Wellcome Trust Institutional Strategic Support Fund; grant 204823/Z/16/Z).

The findings, published April 28 in the journal Nature, suggest that the brain’s drainage system — known as the meningeal lymphatics — plays a pivotal but underappreciated role in neurodegenerative disease, and that repairing faulty drains could be a key to unlocking the potential of certain Alzheimer’s therapies.

“The lymphatics are a sink,” said co-senior author Jonathan Kipnis, PhD, the Alan A. and Edith L. Wolff Distinguished Professor of Pathology & Immunology and a BJC Investigator. “Alzheimer’s and other neurodegenerative diseases such as Parkinson’s and frontotemporal dementia are characterized by protein aggregation in the brain. If you break up these aggregates but you have no way to get rid of the debris because your sink is clogged, you didn’t accomplish much. You have to unclog the sink to really solve the problem.”

Sticky plaques of the protein amyloid start forming in the brains of people with Alzheimer’s two decades or more before symptoms such as forgetfulness and confusion arise. For years, scientists have tried to treat Alzheimer’s by developing therapies that clear away such plaques but have had very limited success. One of the most promising candidates, aducanumab, recently proved effective at slowing cognitive decline in one clinical trial but failed in another, leaving scientists baffled.

Kipnis, who is also a professor of neurosurgery, of neurology and of neuroscience, identified meningeal lymphatics as the brain’s drainage system in 2015. A few years later, in 2018, he demonstrated that damage to the system increases amyloid buildup in mice. He suspects that the mixed and often disappointing performance of anti-amyloid drugs can be explained by differences in lymphatic function among Alzheimer’s patients. But proving this hunch has been challenging, as there are no tools to measure the health of a person’s meningeal lymphatics directly.

In this study, Kipnis and colleagues took an indirect approach to checking the drainage system in the brains of Alzheimer’s patients. The study was undertaken in collaboration with biotherapeutics company PureTech Health.

Thinking that the effects of a clogged drain might spill over onto microglia, the cells that serve as the brain’s cleanup crew, the researchers looked for evidence of lymphatic damage in the form of altered patterns of microglial gene expression. Microglia play a complicated role in Alzheimer’s disease: They seem to slow the growth of amyloid plaques early in the course of the disease but worsen neurological damage later on. The researchers disabled the meningeal lymphatics of a group of mice genetically prone to forming amyloid plaques, leaving the lymphatics functional in another group of mice for comparison, and analyzed the patterns of genes expressed by microglia.

Lymphatic dysfunction shifted microglia toward a state that was more likely to promote neurodegeneration. Further, when co-senior author Oscar Harari, PhD, an assistant professor of psychiatry and of genetics, compared the gene-expression patterns in microglia from mice and people — including 53 people who died with Alzheimer’s disease and nine who died with healthy brains — the people’s microglia most resembled those from mice with damaged lymphatics.

“There was a signature we found in the microglia from mice with ablated meningeal lymphatics,” Harari said. “When we harmonized the human and mouse microglial data, we found the same signature in the human data.”

Another cell type, endothelial cells that line the inside of lymphatic vessels, provided additional evidence for the importance of the brain’s drainage system. Co-senior author Carlos Cruchaga, PhD, a professor of psychiatry, of genetics and of neurology, identified the genes most highly expressed in lymphatic endothelial cells from mice. He discovered that genetic variations in many of the same genes have been linked to Alzheimer’s in people, suggesting that problems with the lymphatics might contribute to the disease.

“In the end, even though we’re looking at specific cell types and specific pathways, the brain is one big organ,” Cruchaga said. “The lymphatic system is how the garbage is cleaned out of the brain. If it’s not working, everything gets gummed up. If it starts working better, then everything in the brain works better. I think this is a very good example of how everything is connected, everything impacts brain health.”

To find out whether bolstering lymphatic function could help treat Alzheimer’s disease, the researchers studied mice genetically prone to developing amyloid plaques and whose lymphatics were impaired due to age or injury. They treated the animals with mouse versions of the experimental Alzheimer’s drugs aducanumab or BAN2401, along with vascular endothelial growth factor C, a compound that promotes the growth of lymphatic vessels. Combination therapy reduced amyloid deposits more than the anti-amyloid drugs alone.

“There have been several antibodies that appear very effective at reducing amyloid deposits in mouse studies and now in humans,” said co-author David Holtzman, MD, the Andrew B. and Gretchen P. Jones Professor and head of the Department of Neurology. “Some now also appear to slow cognitive decline in people with very mild dementia or mild cognitive impairment due to Alzheimer’s. However, the cognitive effects are not large, and one wonders if meningeal lymphatic system dysfunction may be related in part to the somewhat limited effects on cognition currently being observed. The meningeal lymphatic system seems to be influencing not just the progression of the amyloid component of Alzheimer’s pathology but also the response to immunotherapy. Maybe an understanding of this system is a part of what the field of Alzheimer’s drug development has been missing, and with increased attention to it we will better translate some of these promising drug candidates into therapies that provide meaningful benefits to people living with this devastating disease.”

And now comes the first major payoff from the Vertebrate Genome Project (VGP): near complete, high-quality genomes of 25 species, Howard Hughes Medical Institute (HHMI) Investigator Erich Jarvis with scores of coauthors report April 28, 2021, in the journal Nature. These species include the greater horseshoe bat, the Canada lynx, the platypus, and the kākāpō parrot — one of the first high-quality genomes of an endangered vertebrate species.

The paper also lays out the technical advances that let scientists achieve a new level of accuracy and completeness and paves the way for decoding the genomes of the roughly 70,000 vertebrate species living today, says HHMI Investigator and study coauthor David Haussler, a computational geneticist at the University of California, Santa Cruz (UCSC). “We will get a spectacular picture of how nature actually filled out all the ecosystems with this unbelievably diverse array of animals.”

Together with a slew of accompanying papers, the work is beginning to deliver on that promise. The project team has discovered previously unknown chromosomes in the zebra finch genome, for example, and a surprise finding about genetic differences between marmoset and human brains. The new research also offers hope for saving the kākāpō parrot and the endangered vaquita dolphin from extinction.

“These 25 genomes represent a key milestone,” explains Jarvis, VGP chair and a neurogeneticist at The Rockefeller University. “We are learning a lot more than we expected,” he says. “The work is a proof of principle for what’s to come.”

From 10K to 70K

The VGP milestone has been years in the making. The project’s origins date back to the late-2000s, when Haussler, geneticist Stephen O’Brien, and Oliver Ryder, director of conservation genetics at the San Diego Zoo, figured it was time to think big.

Instead of sequencing just a few species, such as humans and model organisms like fruit flies, why not read the complete genomes of ten thousand animals in a bold “Genome 10K” effort? At the time, though, the price tag was hundreds of millions of dollars, and the plan never really got off the ground. “Everyone knew it was a great idea, but nobody wanted to pay for it,” recalls HHMI Investigator and HHMI Professor Beth Shapiro, an evolutionary biologist at UCSC and a coauthor of the Nature paper.

Plus, scientists’ early efforts at spelling out, or “sequencing,” all the DNA letters in an animal’s genome were riddled with errors. In the original approach used to complete the first rough human genome in 2003, scientists chopped up DNA into short pieces a few hundred letters long and read those letters. Then came the fiendishly difficult job of assembling the fragments in the right order. The methods weren’t up to task, resulting in misassemblies, major gaps, and other mistakes. Often it wasn’t even possible to map genes to individual chromosomes.

The introduction of new sequencing technologies with shorter reads helped make the idea of reading thousands of genomes possible. These rapidly developing technologies slashed costs but also reduced quality in genome assembly structure. Then in 2015, Haussler and colleagues brought in Jarvis, a pioneer in deciphering the intricate neural circuits that let birds trill new tunes after listening to others’ songs. Jarvis had already shown a knack for managing big, complex efforts. In 2014, he and more than a hundred colleagues sequenced the genomes of 48 bird species, which turned up new genes involved in vocal learning. “David and others asked me to take on leadership of the Genome 10K project,” Jarvis recalls. “They felt I had the personality for it.” Or, as Shapiro puts it: “Erich is a very pushy leader, in a nice way. What he wants to happen, he will make happen.”

Jarvis expanded and rebranded the Genome 10K idea to include all vertebrate genomes. He also helped launch a new sequencing center at Rockefeller that, together with one at the Max Planck Institute in Germany led by former HHMI Janelia Research Campus Group Leader Gene Myers, and another at the Sanger Institute in the UK led by Richard Durbin and Mark Blaxter, is currently producing most of the VGP genome data. He asked Adam Phillippy, a leading genome expert at the National Human Genome Research Institute (NHGRI), to Chair the VGP assembly team. Then, he found about 60 top scientists willing to use their own grant money to pay for the sequencing costs at the centers to tackle the genomes they were most interested in. The team also negotiated with the Māori in New Zealand and officials in Mexico to get kākāpō and vaquita samples in “a beautiful example of international collaboration,” says Sadye Paez, program director of the VGP at Rockefeller.

Opening doors

The massive team of researchers pulled off a series of technological advances. The new sequencing machines let them read DNA chunks 10,000 or more letters long, instead of just a few hundred. The researchers also devised clever methods for assembling those segments into individual chromosomes. They have been able to tease out which genes were inherited from the mother and the father. This solves a particularly thorny problem known as “false duplication,” where scientists mistakenly label maternal and paternal copies of the same gene as two separate genes.

“I think this work opens a set of really important doors, since the technical aspects of assembly have been the bottleneck for sequencing genomes in the past,” says Jenny Tung, a geneticist at Duke University, who was not directly involved with the research. Having high-quality sequencing data “will transform the types of question that people can ask,” she says.

The team’s improved accuracy shows that previous genome sequences are seriously incomplete. In the zebra finch, for example, the team found eight new chromosomes and about 900 genes that had been thought to be missing. Previously unknown chromosomes popped up in the platypus as well, as members of the team reported online in Nature earlier this year. The researchers also plowed through, and correctly assembled, long stretches of repetitive DNA, much of which contain just two of the four genetic letters. Some scientists considered these stretches to be non-functional “junk” or “dark matter.” Wrong. Many of the repeats occur in regions of the genome that code for proteins, says Jarvis, suggesting that the DNA plays a surprisingly crucial role in turning genes on or off.

That’s just the start of what the Nature paper envisions as “a new era of discovery across the life sciences.” With every new genome sequence, Jarvis and his collaborators uncover new — and often unexpected — findings. Jarvis’s lab, for example, has finally nabbed the regulatory region of a key gene parrots and songbirds need to learn tunes; next, his team will try to figure out how it works. The marmoset genome yielded several surprises. While marmoset and human brain genes are largely conserved, the marmoset has several genes for human pathogenic amino acids. That highlights the need to consider genomic context when developing animal models, the team reports in a companion paper in Nature. And in findings also published last year in Nature, a group led by Professor Emma Teeling at University College Dublin in Ireland discovered that some bats have lost immunity-related genes, which could help explain their ability to tolerate viruses like SARS-CoV-2, which causes COVID-19.

The new information also may boost efforts to save rare species. “It is a critically important moral duty to help species that are going extinct,” Jarvis says. That’s why the team collected samples from a kākāpō parrot named Jane, part of a captive breeding program that has brought the parrot back from the brink of extinction. In a paper published in the new journal Cell Genomics, of the Cell family of journals, Nicolas Dussex at the University of Otago and colleagues described their studies of Jane’s genes along with other individuals. The work revealed that the last surviving kākāpō population, isolated on an island off New Zealand for the last 10,000 years, has somehow purged deleterious mutations, despite the species’ low genetic diversity. A similar finding was seen for the vaquita, with an estimated 10-20 individuals left on the planet, in a study published in Molecular Ecology Resources, led by Phil Morin at the National Oceanic and Atmospheric Administration Fisheries in La Jolla, California. “That means there is hope for conserving the species,” Jarvis concludes.

A clear path

VGP is now focused on sequencing even more species. The project team’s next goal is finishing 260 genomes, representing all vertebrate orders, and then snaring enough funding to tackle thousands more, representing all families. That work won’t be easy, and it will inevitably bring new technical and logistical challenges, Tung says. Once hundreds or even thousands of animals readily found in zoos or labs have been sequenced, scientists may face ethical hurdles obtaining samples from other species, especially when the animals are rare or endangered.

But with the new paper, the path ahead looks clearer than it has in years. The VGP model is even inspiring other large sequencing efforts, including the Earth Biogenome Project, which aims to decode the genomes of all eukaryotic species within 10 years. Perhaps for the first time, it seems possible to realize the dream that Haussler and many others share of reading every letter of every organism’s genome. Darwin saw the enormous diversity of life on Earth as “endless forms most beautiful,” Haussler observes. “Now, we have an incredible opportunity to see how those forms came about.”