Harvard and Yale Researchers Awarded $46 Million to Study Autism’s Origin in the Brain

Two Harvard Medical School researchers and one Yale University professor were awarded a $46 million grant from a privately funded autism initiative to study how the condition first emerges in the developing human brain, according to an HMS announcement last week.

The award comes from Aligning Research to Impact Autism, a philanthropic effort launched in 2024 to fund research on autism and accelerate the development of treatments. It will fund four linked projects and ARIA’s new Human Developmental Neurobiology Hub, which will be co-led by Stem Cell and Regenerative Biology professor Paola Arlotta and Nenad Sestan, a neuroscience professor at the Yale School of Medicine.

Yale announced in late August that its share of the award totals nearly $25 million.

Arlotta’s lab will grow brain organoids — three-dimensional tissue models derived from patients’ stem cells — to observe developmental processes that cannot be studied directly in humans. The approach lets researchers study early brain development across large groups of people with and without autism, using tissues grown from their own cells.

HMS professor Marinka Zitnik will lead the hub’s artificial intelligence work, building models that integrate data across genes, cell types, brain regions, and patient records to flag biomarkers and rank potential drug targets.

Arlotta, who has studied brain development for about 15 years, said the grant’s scale and its link to clinical data distinguish it from her previous work.

“What is different with this grant is that it allows really us to connect with the clinic in ways that we couldn’t do before,” Arlotta said. “It’s a scale that is unprecedented, and the hope is that this would really allow us to identify this element of convergence across genetic states and patients.”

The award lands as Harvard researchers continue to weigh their reliance on federal support.

The Trump administration froze roughly $2.7 billion in federal grants and contracts to the University in 2025 after Harvard rejected a series of government demands tied to campus protests, academics, and admissions policy.

A federal judge struck down the freeze in September 2025, and most of the money returned to Harvard’s accounts within weeks, but the administration’s appeal remains pending before the First Circuit.

ARIA has already put significant money into Harvard’s Longwood campus. Boston Children’s Hospital, an HMS affiliate, received up to $17.25 million in June to join ARIA’s clinical trial network as a study site, following a $7.5 million award in December 2025 to help run the network’s coordinating center.

Arlotta said that, while she welcomes private funding, she does not see it as a substitute for federal support.

She also credited ARIA with treating the work as a joint effort.

“What we’re trying to do here as scientists is to move really the field of knowledge forward, such that we might be able to address therapeutically some of the most devastating diseases of our time,” Arlotta said. “It’s really truly a collaboration between the scientists and the funders towards this goal. We are equally important, and these kinds of investments are key for the betterment of society.”

Asked about the risks of applying AI to medical data — including bias and the difficulty of explaining how models reach their conclusions — Arlotta said the technology’s value lies in allowing the lab to test a greater number of therapeutic hypotheses than would otherwise be possible. But she cautioned that it remains unclear how transformative the models will prove to be, and how quickly.

The Harvard team will focus on developing organoids and preparing the resulting data for machine learning. At Yale, Sestan’s lab will conduct two projects. The first will involve creating several high-resolution models showing how the brain develops across a lifetime, while the second will explore how genes are expressed in the human brain at different stages of development.

Arlotta called that division of labor the “secret sauce in science for great discovery.”

“You have to come together from different fields, and you need to be able to work with colleagues that you know share this vision and are there to move the field forward,” Arlotta said. “Science is not siloed. Perhaps it was at some point in time in the past, but certainly not now, and certainly not in the future.”

—Staff writer Riya S. Shah can be reached at [email protected] and on Signal at riyas.23. Follow her on X @RiyaShah233.

—Staff writer Juliana L. Yao can be reached at [email protected] and on Signal at jly.87. Follow her on X @JulianaYao298.