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The Brief

The most important stories for you to know today
  • Clogged checkpoints hurt U.S.-Mexico border towns
    Clothing on mannequins on a sidewalk have handwritten prices
    A clothing store in the San Ysidro neighborhood of San Diego on April 16, 2024.

    Topline:

    U.S.-Mexico border checkpoints remain severely clogged — and border communities are hurting.

    Why now: In recent months lines at the border often stretched for several hours, frustrating more than 150,000 students, cross-border families, health care workers, small business owners, and others who daily cross to and from Mexico.

    Why it matters: Experts say some fronterizas have stopped crossing the border as often, and the loss of foot traffic in the region has resulted in heavy sales losses for small businesses.

    Government agencies are spending billions of dollars to improve wait times at the U.S.-Mexico border, but the checkpoints remain severely clogged — and border communities are hurting.

    Lea esta historia en Español

    In recent months lines at the border often stretched for several hours, frustrating more than 150,000 students, cross-border families, health care workers, small business owners, and others who daily cross to and from Mexico. Experts say some fronterizas have stopped crossing the border as often, and the loss of foot traffic in the region has resulted in heavy sales losses for small businesses.

    “Money we can replace, but time will never come back. Those people are wasting their time in that line,” said Sunil Gakherja, 49, who owns a small perfume store in San Ysidro, a neighborhood in San Diego, close to the border.

    U.S. border officials point to the need to shift resources to handle irregular migration — people who come into the United States in places other than official ports of entry, usually to seek asylum. San Diego surpassed Tucson this month as Border Patrol’s busiest sector in the nation.

    But border-area residents and business leaders say the federal government should staff the border effectively so that the $741-million expansion of the San Ysidro Port of Entry has its intended impact, to reduce wait times and stimulate the regional economy.

    Research published by the Atlantic Council says a 10-minute reduction in wait times could lead to an additional $26 million worth of cargo entering the United States each month and an annual impact of $5.4 million on the U.S. economy from purchases by families and individuals entering the United States from Mexico.

    In the San Diego region, regular border crossers say wait times are going up, not down. Waits that used to last 30 minutes to an hour on weekdays can now regularly take three to four hours. On several days last December, pedestrians waited six hours or more. Adding to their frustration, long lines also stretch southbound to enter Mexico.

    “Devastating” is how Kenia Zamarripa described the waits on both sides of the border. She is vice president of international and public affairs at the San Diego Regional Chamber of Commerce.

    “This is families losing their incomes,” she said. “There are 800 small businesses in San Ysidro that depend on pedestrian crossings and, again, 90% of their customers cross on foot.”

    State officials said it’s unclear how much California has missed out on in sales tax revenue because that information can’t be broken down by zip code.

    Small border businesses suffering

    After opening in 2017, the El Rincon restaurant in San Ysidro faced the same challenges and growing pains many small, family-run businesses contend with, said Andrea Alaniz. Her mom owns the Mexican food restaurant along San Ysidro Boulevard, a few blocks from the border.

    “We just opened the doors, and it was just us doing the cooking and waiting tables — hoping that business would increase and keep on a nice trend,” she recalled.

    Word quickly spread of her mother’s caseros — homemade family recipes from Guadalajara, Jalisco. Lines would wrap around the tiny restaurant, with some customers even driving from Los Angeles or crossing north from Baja California, for the food.

    “You know, the spices … you can find the spices anywhere, but really, it’s the way my mom and my family cooks,” said Alaniz. “My mom’s an amazing cook, and our recipes … they go way back.”

    The whole family — five siblings — pitched in to handle the increased volume and their newfound success.

    “We all work here,” laughed Alaniz. “It was a Sunday, and I remember we were all here, and the music was blaring, and we were just dancing and having fun and it was a really nice feeling.”

    Then the pandemic hit. Federal officials restricted cross-border travel. Business tanked. About 200 businesses closed in San Ysidro, a working-class, mostly immigrant community of about 25,000 people, said Jason Wells, president of the local chamber of commerce.

    “Shut their doors forever. Gone,” he said.

    Alaniz and her family managed to stay open and even sent some money home to family in Mexico, but it was a daily fight. “We just don’t get the same amount of people coming in, because people aren’t going back and forth anymore,” said Alaniz.

    Multiple studies show immigrants like Alaniz’s family were a key economic engine for the United States’ rebound from the pandemic. Some 50% of the labor market’s recent growth came from foreign-born workers between January 2023 and January 2024, according to an Economic Policy Institute analysis of federal data.

    Zamarripa says it’s these same border communities that lose about $2 billion yearly because of excessive border wait times. She worries the latest bottlenecks at checkpoints could severely impact those struggling to get back on their feet.

    Gakherja, the owner of the perfumery, described a Sunday customer who waited six hours to cross the border.

    “He got in the line at 9 in the morning, and he got here at 3:30 p.m. It’s too much. Imagine they have kids who have to go to the restroom. They need food. They’re not thinking about shopping after that,” said Gakherja.

    Waiting is the hardest part

    It’s not just small businesses that are hurting. Those hardest hit by backlogs at inefficient ports of entry include the region’s hospitality and hospital workers, students, medical patients, and anyone who relies on the interdependence of a cross-border region to offset the skyrocketing costs of living in San Diego, one of the most expensive cities in the nation.

    Hector Urquiza, a 19-year-old college student serving in the Army Reserves, lives with his brother in Tijuana because rent is too expensive in San Diego.

    “When I had to go to work, there was a two-hour line. It was like a snake, you know, wiggling around. That was kind of painful,” said Urquiza.

    Cross-border travelers often turn to Facebook to document their experiences and wait times because the official Customs and Border Protection data is considered inaccurate and unreliable. Cómo está la línea Tijuana (How is the Tijuana line), a Facebook group with 430,000 members, was founded in June 2013 when its creator relied on the official CBP wait times and was extraordinarily late for work, according to his posts.

    Urquiza said people who regularly cross the border develop a system. It sometimes includes holding a spot in line for each other to cut down on their day-to-day commute, but Tijuana authorities recently have cracked down on the practice, making it harder to get through the school or work week.

    “Like you can tell somebody to save your spot, but when you try to go back to your spot, the police are like, ‘Nah, no amigo’,” he said.

    When commuters wait in border traffic for hours, business productivity across Southern California suffers, say local leaders.

    “As a business owner, you can’t expect an employee to perform at 100% if he has four hours of sleep and then six hours on foot,” said Joaquín Luken, executive director of the Smart Border Coalition, which aims to streamline border crossings.

    Wait times averaged three hours to get back into Mexico in mid-March, he said.

    “You have a complete shift of the profile of a crosser,” said Luken.

    Before, people would cross to shop, eat, or visit. But now, border crossings are strictly business—people who need to cross for school, work, or care for a family member.

    “So, of course, most of the businesses here in the South Bay are struggling, and this impact does trickle up the county,” he said of San Diego County.

    Reece Rackley, a 30-year-old who lives in Clairemont, crosses the border to see a doctor in Baja California to save money on medical care. She’s one of roughly 1 million Americans who travel to Mexico yearly to save on health care.

    Waiting in long lines to return home can be “very, very frustrating,” she said.

    Victor Navarro, 27, a social worker and student at San Diego City College, recently broke down crying when asked about the long waits.

    “I’ve lost at least two or three years of my life in that line,” said Navarro, who lives in the La Postal neighborhood of Tijuana.

    “Why is that happening? Do they hate us? Do they want us to be standing there in line? Are they humiliating us?” asked Navarro.

    Does the U.S.-Mexico border need to be this way?

    As President Joe Biden worked to salvage a border deal with Congress in January, he said he would “shut down” the U.S.-Mexico border. His words echoed former President Donald Trump, who threatened in 2019 to close the border if Mexico didn’t step up its immigration enforcement.

    People in the Cali-Baja region wish officials in Washington would stop saying that.

    “Number one, you can’t close a border,” said Luken. “Especially when you look at Mexico being the U.S.’s number one trading partner.” One in every 29 workers in the United States has a job created or supported by U.S.-Mexico trade, the 2022 Atlantic Council study shows.

    On Monday, many commuters woke at 1 a.m. to get into a four-hour line. When they finally arrived at the checkpoint just before dawn, they found less than a third of Customs and Border Protection’s available booths were open. Some wondered aloud whether the traffic nightmare wasn’t just a slow-moving demonstration of Washington’s threats.

    Customs and Border Protection has said it shifted resources to handle large groups of migrants who overwhelm border officials to cross into the United States.

    “CBP has taken significant steps to surge personnel and resources to impacted sectors and address the challenges we are experiencing across the southwest border,” a Department of Homeland Security official said in January.

    Border officials also are trying to make sure fentanyl doesn’t enter the country.

    Luken, of the Smart Border Coalition, said when officers take an extra three seconds to open and shut a car door, multiplied by the 150,000 to 160,000 people who cross daily, it’s easy to see how wait times are compounding.

    Customs and Border Protection officials recently declined an interview with CalMatters, but Homeland Security officials have acknowledged that frustrated daily commuters and excessively long border lines highlight a need for funding to address what Washington has described as a border crisis.

    “CBP will continue to evaluate the situation along the border and make operational changes as necessary,” Homeland Security said in a statement. “Stakeholders will be provided with operational updates as they become available.”

    The Homeland Security statement also put some of the blame on people entering the United States irregularly and the people who smuggle them in.

    “Encounter numbers continue to fluctuate as smugglers and bad actors continue to spread falsehoods and show complete disregard for the safety and wellbeing of vulnerable migrants,” the agency said. “The fact remains: the United States continues to enforce immigration law, and our borders are not open for those without a legal basis to enter the country.”

  • Unhoused man died after entering interim housing
    Exterior of the Mayfair hotel in Koreatown
    Raz Chowdhury, a 45-year-old unhoused man, died at The Mayfair in July 2026 after being moved to hotel as part of the Inside Safe program.

    Topline:

    45-year-old Raz Chowdhury was moved off the streets into interim housing through an Inside Safe operation. A week later, he was found dead in his hotel room.


    The backstory: L.A. Mayor Karen Bass’ office said it does not disclose the locations where an individual is placed following an Inside Safe operation. According to Ktown for All, Chowdhury died at the Mayfair Hotel in Westlake, which is used for interim housing.

    A spokesperson for the Los Angeles County Department of Medical Examiner said the case is still under investigation and Chowdhury died at a hotel in the 1200 block of West 7th Street.

    This story first appeared on The LA Local.

    A week after 45-year-old Raz Chowdhury was moved off the streets into interim housing through an Inside Safe operation, he was found dead in his hotel room.

    Chowdhury had spent years living on the streets of Koreatown, moving between encampments along Sixth Street and Wilshire Boulevard and Manhattan Place.

    Sherin Varghese first met him three or four years ago. Chowdhury would reach out to Varghese, a volunteer with Ktown for All, an advocacy group that provides direct aid for people experiencing homelessness in Koreatown. He would ask her for tents, tarps, clothes and other supplies. More often than not, she said, they weren’t for him.

    “He would always go above and beyond to take care of the people around him,” Varghese said at a vigil for Chowdhury on Saturday, Aug. 29.

    Once, after Chowdhury lost his phone during a sanitation sweep, he searched for Varghese online and found her work number. He called to ask if she could bring tents and tarps for him and other people whose belongings were lost in the sweep.

    “He was resourceful, he was reliable, and he was so thoughtful about the way that he talked about how all of this affected him and affected his friends,” Varghese said.

    On June 25, Chowdhury was among 31 people moved into housing during an Inside Safe operation at Wilshire Boulevard and Manhattan Place, according to Mayor Karen Bass’ office.

    A week later he was dead.

    What happened after Inside Safe

    According to Ktown for All, Chowdhury died at the Mayfair Hotel in Westlake, which is used for interim housing.

    A spokesperson for the Los Angeles County Department of Medical Examiner said the case is still under investigation and Chowdhury died at a hotel in the 1200 block of West 7th Street on July 2. His cause of death is listed as deferred and the case is under investigation by the Los Angeles Police Department’s Rampart Division.

    The Los Angeles Homeless Services Authority, which oversees the Mayfair, would not say if Chowdhury was a resident when he died. An agency spokesperson said they cannot confirm an individual’s enrollment in a LAHSA-contracted program without a written release from next of kin.

    LAHSA’s latest Inside Safe report shows that 6,406 people had entered interim housing through the program as of July 31. About 1,750 people remained in interim housing, including 289 at the Mayfair. Meanwhile, 1,802 people, or more than one in four who entered the program, had returned to homelessness. Another 126 people, or about 2%, were listed as deceased.

    Bass’ office said it does not disclose the locations where an individual is placed following an Inside Safe operation.

    Once someone is connected to interim housing, ongoing services and case management are handled by a LAHSA-contracted service provider, mayor spokesperson Jieun Kim said.

    Remembering Chowdhury

    The people who knew Chowdhury gathered last week to remember him at the site of the encampment where he had lived at Wilshire Boulevard and Manhattan Place.

    A little more than two dozen people attended the memorial, where they placed flowers at the base of a small tribute to him.

    Planters now line the sidewalk where the tents once were. Several people cried as they shared memories of Chowdhury, who they said spent years looking out for others living on the streets of Koreatown.

    Cynthia Zhang, who has volunteered with Ktown for All for about four to five years, remembers visiting an encampment where Chowdhury was staying after the Los Angeles fires. Newly displaced people there told her they felt safer with that community than they did at shelters.

    “I think Raz was really instrumental in helping create that kind of space,” Zhang said at the vigil.

    The last time Zhang saw Chowdhury, he had moved again and did not have a lot of his stuff. But he had a new puppy named T-Rex and seemed to be in good spirits.

    “He had a really lovely smile,” Zhang said. “I just remember him skateboarding around … all these little things, maybe because I didn’t see him every day, it really does feel like I’ll be walking around and I’ll see him in one of our old spots.”

    David Strugar, another longtime Ktown for All volunteer, said Chowdhury was often the person volunteers went to when they wanted to know how people in the area were doing.

    “I would always point him out and say, ‘That’s the mayor of this area,’ because wherever he was, he was just the center of it, and he took care of people,” Strugar said.

    Chowdhury would tell volunteers who needed what and help distribute supplies, Strugar said.

    A few weeks before he died, Varghese said, she and Chowdhury were looking for places where he could stay outside a 41.18 zone, where the city restricts sitting, lying, sleeping and storing personal property in certain public rights-of-way under specified circumstances.

    Then Inside Safe moved him indoors.

    “I hoped that he’d be one of its success stories, but a week later, he was gone,” Varghese said. “The program is called Inside Safe, but for Raz and 125 others, it wasn’t that. And it was never going to be Inside Safe, and it was never going to be easy to be inside alone for someone who had so much to give and always surrounded himself with people to take care of.”

    The last time Strugar saw Chowdhury, he had his dog T-Rex with him. Ktown for All volunteers don’t know where T-Rex is now.

    Chowdhury believed he had the right to community and companionship, Strugar said.

    “And there are so many people who have so much and won’t give anything,” Strugar said. “And Raz kept having everything taken away from him, and he still ended up being the person to give.”

    He added, “I just keep expecting to walk around the corner and see him, and I’m angry that I won’t.”

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  • SoPas doctor makes backyard roast for fun
    An Asian man wearing glasses and an apron holds a roasted duck above a big outdoor oven.
    Hong Pham, aka That Peking Duck Guy, takes a roasted Pipa duck out of his outdoor oven.

    Topline:

    Radiologist Hong Pham has an unusual side hustle — cooking and selling Peking and roast ducks from his South Pasadena backyard.

    The backstory: That Peking Duck Guy started out as a social media account documenting Pham's culinary journey to make the perfect duck. It then became a side hustle when strangers and neighbors offered to buy his birds.

    Read on ... to learn about how Pham got started and how he cooks his ducks.

    Got a taste for ducks cooked the Chinese way? Your quest may take you to a quiet suburban backyard in South Pasadena.

    That's where That Peking Duck Guy cooks and sells his birds. His clients, he said, include Phil Rosenthal and Roy Choi.

    The guy behind That Peking Duck Guy is Hong Pham, who started the social media account in late 2025 as a way to document his latest culinary obsession: making the perfect duck, be it Peking or Pipa (deboned and flattened into the shape of the namesake Chinese string instrument).

    The intention was not to sell. "I have a day job," Pham said. A radiologist, to be precise.

    "I was actually making so many that neighbors wanted to claim it and offered to buy it," he added. "So I'm like, 'OK, that makes it easier 'cause I don't have to eat it all.'"

    Soon came DMs from strangers asking for the same thing.

    These days, That Peking Duck Guy caters events and holds takeout pop-ups where people can purchase and pick up a duck (which comes with sides and duck soup) from his South Pasadena backyard — right where he cooks them.

    A plate of duck served with Chinese sweet sauce, chopped spring onions and cucumber slices.
    Peking duck from That Peking Duck Guy served with Chinese sweet sauce, chopped spring onions and cucumber slices.
    (
    Fiona Ng
    /
    LAist
    )

    Duck is the latest obsession

    Duck is not his first rodeo. Pham said he and his wife are foodies who've always been curious about delving into Vietnamese and other Asian culinary traditions. For Pham, that also means replicating some of these dishes at home, from scratch.

    He'd gone on a tofu bender — making gallons of the stuff, as blocks, drinks and pudding — and also a bánh cuốn spree, or Vietnamese steamed rice rolls. He landed on duck as his latest subject only because he had wanted to make better heo quay, or Vietnamese roasted pork belly.

    It's the oven

    An Asian man in glasses and an apron smiling next to a spaceship-like outdoor oven.
    Pham and one of his special outdoor ovens he uses to roast duck.
    (
    Fiona Ng
    /
    LAist
    )

    He researched how to get that extra crisp online and landed on an oven people in Asia use to make roast and Peking ducks.

    How to get your duck

    Pham hosts takeout pop-ups from South Pasadena backyard. Follow That Peking Duck Guy's Instagram for updates.

    Visit the official website for catering requests.

    "It was called the Apollo oven 'cause it looks like an Apollo space capsule," he said.

    He bought one and then another. In between, he experimented cooking different meats with the new oven to get a feel before turning to the waterfowl.

    He even got advice from Top Chef winner Mei Lin, whom he messaged cold: "She's like, 'Keep it simple. Keep it basic. Keep it traditional.'"

    Three ducks inside an outdoor oven
    Three Pipa ducks inside the oven.
    (
    Fiona Ng
    /
    LAist
    )

    Hundreds of ducks later, Pham said he still learns something new. That's one reason why his side hustle has stuck around.

    "I didn't create like, you know, That Bánh Cuốn Man," he said. "Yeah, duck's gonna last."

    How That Peking Duck Guy cooks his ducks

    Pham starts 7 to 10 days before cooking. Here's the preparation process:

    1. He usually trims off the legs and the wings, because those parts get burnt in the oven.
    2. He insufflates the duck. He sticks an air pump in between the meat and the skin to separate the two, so the entire duck blows up into a "huge balloon essentially," he said.
    3. He scalds the skin with a combination of vinegar and maltose to make it "aerodynamic and tight" to get that crispiness.
    4. He seasons the inside of the duck.
    5. He then hangs and dries the ducks for about 7 to 10 days.
    6. Then in the Apollo oven they go. Peking ducks take about an hour and 15 minutes to cook. Pipa ducks take about 40 minutes.

    When does he know they're done? "Well, you know the color, we're looking for that beautiful mahogany glistening skin, you know?" Pham said.

    Two freshly cooked roast ducks.
    Two Pipa ducks fresh out of the oven.
    (
    Fiona Ng
    /
    LAist
    )

  • SoCal is a launchpad
    A sign of the company Miniso's red shopping bag logo.
    A MINISO logo is displayed on a sign outside of a store in San Diego.

    Topline:

    SoCal has become a proving ground for some of the country’s fastest-growing Asian and Asian American retailers, giving chains like Miniso and 99 Ranch Market an early test of broader U.S. appeal.

    Growing fast: On the National Retail Federation’s 2026 Hot 25 list, Miniso ranks No. 1, Daiso No. 3, Uniqlo parent Fast Retailing No. 6 and 99 Ranch Market No. 15.

    Backstory: All four have had a Southern California presence for years, giving them experience in one of the country’s most diverse and competitive retail markets.

    Southern Californians who’ve long shopped at Daiso, Miniso, Uniqlo or 99 Ranch Market may not be surprised to see the Asian-rooted chains expand across the country.

    But that growth is now showing up in the numbers.

    The National Retail Federation’s Hot 25 Retailers list ranks retailers by U.S. sales growth from 2024 to 2025. Miniso tops the list, with sales up nearly 53%.

    The Chinese chain of gift shops opened its first U.S. store in Pasadena’s Old Town more than nine years ago and is now aiming to grow its American footprint to nearly 500 stores this year.

    “If you can make it in Southern California, that's great,” said David Marcotte, senior vice president of global retail and technology at Kantar and an author of the NRF list.

    A store clerk gathers grocery carts outside a 99 Ranch supermarket
    A 99 Ranch market opened in 2023 in Eastvale.
    (
    Gina Ferazzi
    /
    Los Angeles Times via Getty Images
    )

    Marcotte says succeeding in California’s highly competitive retail market can teach chains lessons that translate elsewhere.

    “The stone-cold reason is quality. The second one is experience,” he said. “Those are the two things that when shoppers go into any retailer, they’re looking for.”

    Daiso ranks third, with growth of nearly 26%, while another Japanese company, Fast Retailing — the parent company of Uniqlo — comes in sixth.

    99 Ranch Market, an American supermarket chain founded in Orange County that specializes in Asian groceries, comes in 15th.

    Marcotte says Southern California has been a logical landing spot for these companies because of its proximity to Asia. But Marcotte says it can also be an unforgiving place to launch because of the competition, and he often encourages the clients he advises to consider smaller markets.

    “I said if you open in Southern California, open one store, get it right,” Marcotte said. “If you get it wrong, you're dead. You'll never recover. You'll have to leave the country and come back in.”

    The supermarket industry is particularly tough to break into because customers here, he says, have plenty of alternatives if the quality, selection or experience falls short.

    He also emphasizes a retailer in California focused on Asian goods will see more success serving Chinese, Filipino and other Asian customers rather than designing around a particular ethnic group.

    “That type of diversity of Asian customers that you have to address in the same store is what really proves to be the difference for an Asian retailer in the California market,” Marcotte said.

    That’s part of the business model for 99 Ranch, which was founded by a Taiwanese immigrant who opened the first location in Westminster's Little Saigon in 1984.

  • UC scientists map interactions in new research

    Topline:

    Scientists have now gotten closer to understanding how gene mutations may lead some people to develop profound autism.

    Why it matters: A team of researchers from UC San Francisco mapped more than a thousand interactions between many proteins that come from certain autism risk genes.

    Why now: This molecular atlas, published in the journal Science, could point researchers toward new and promising treatments.

    Scientists have now gotten closer to understanding how gene mutations may lead some people to develop profound autism.

    The clues, they say, lie in the murky space between genes and disease — where key proteins come together and interact.

    A team of researchers from UC San Francisco mapped more than a thousand interactions between many proteins that come from certain autism risk genes. This molecular atlas, published in the journal Science, could point researchers toward new and promising treatments.

    "It's an unprecedented resource for the field," says Dr. Daniel Geschwind, a professor of human genetics, neurology, and psychiatry at UCLA who was not involved with the study. "A lot of people interested in understanding autism and drug development are going to be using this."

    For families affected by profound autism, it offers hope for eventual drug therapies. "This is the kind of scientific advance we have been waiting for and praying for," says Alison Singer, president of the nonprofit Autism Science Foundation, who has a daughter with severe cognitive impairment. "There's still a lot of work ahead, [but] this paper makes the path from genetic discovery to treatment much clearer."

    The work builds on progress made in recent years to identify single genes that harbor mutations found in a subset of individuals with profound autism.

    Getting past the "wall"

    People with profound autism often live with severe intellectual disability and require around-the-clock care. They're nonverbal or minimally verbal, and often have serious medical conditions like epilepsy.

    Pinning down the biology behind profound autism has always been a complicated endeavor — while both genes and environmental factors play a role, those factors can vary widely from person to person.

    In the past decade or so, some genetics researchers have had remarkable success in identifying high-impact genetic differences in a subset of people with profound autism.

    "They've discovered several hundred genes and corresponding mutations that are prevalent in [these] individuals," says Nevan Krogan, director of the Quantitative Biosciences Institute at UC San Francisco.

    "But they kind of hit a wall," he added — because scientists haven't been able to turn those gene discoveries into many promising drugs and treatments.

    "There was this huge missing piece," says Dr. Matthew State, a clinical psychiatrist and geneticist at UCSF: The genes serve as blueprints for making proteins that drive brain development, but researchers lacked visibility into how those proteins do the work.

    State has been a pioneer in identifying high-risk genes, and the mutations in those genes, that are associated with profound autism. Krogan has been at the forefront of using new technology to look into protein interactions.

    More than a decade ago, the two researchers were introduced by their mutual boss, the chancellor at UCSF, who encouraged them to collaborate. "[State] had the genes and the mutations. I had the technologies to look at the corresponding proteins," Krogan says.

    They focused on filling a knowledge gap. "What we've been missing is the mechanistic understanding of how these mutations [on the genes] are seemingly resulting in autism," Krogan says. "In order to understand that, you need to go to the proteins."

    Proteins are the complex molecules that come together to build the body, based on instructions encoded in the genes. "What makes an eye cell an eye cell, and a muscle a muscle, are the proteins and how they work together," State says. "They are the machinery of life."

    In this case, the researchers wanted to find the molecular machinery of profound autism — to understand which proteins came from those high-risk autism genes, and how those proteins worked together.

    The research was slow at first, but more recent advances in technology — including artificial intelligence — have sped things up.

    To start, the researchers went on a "fishing expedition" for protein interactions. They chose 100 proteins from these high-risk autism genes, injected them into lab-grown cells, and then pulled them out, along with the additional proteins that attached to them.

    Then, they used an AI system called AlphaFold, developed by Google DeepMind, to help determine which proteins in the clumps were directly touching. "Where AI is playing an important role is being predictive about who's talking to who," says Krogan. "Sometimes they take years to figure out. Now, we can get these insights in an hour." While imperfect, the system has worked well enough to save significant time and money, Krogan says.

    Then, they wanted to see what happened to the proteins when the genes got tweaked. They introduced mutations that appear in patients with profound autism, and assessed what changed. "We broke the proteins in the way that they're broken in autism," says State. "That allows us ultimately to answer the question of, when they're going wrong in autism, how are they going wrong?"

    They conducted this research in frogs and in organoids, which are lab-grown tissues that model the human brain. In one example, the mutations weakened the connection between two proteins related to which genes turn on and off in a cell. Then, one went rogue, turning on other genes that led to neurodevelopmental defects in organoids.

    Molecular convergence

    There are hundreds of rare, high-risk autism genes, acting in more than a thousand different ways.

    But in mapping more than 1,800 protein interactions, the researchers found that many of them moved along shared biological pathways — particularly those related to early brain development, such as how synapses get constructed, and which neurons develop and when.

    The convergence found in this study aligns with other recent publications, adding to an emerging understanding in the field, says Dr. Geschwind of UCLA.

    "If we look at multiple mutations and they converge on the same process, that's strong evidence that you're dealing with the things that you want to treat," State says.

    Identifying this more limited set of protein complexes that likely contribute to the development of profound autism could change the approach to treatments, says Singer with the Autism Science Foundation. "We've been working gene-by-gene to correct mutations," she says.

    And if future drugs could target these shared protein pathways, she adds, "we may not need that separate therapeutic strategy for every autism gene."

    Setting sights on new drug-development targets

    It takes years to go from a biological discovery like this to an approved drug that treats humans. The findings would need to be translated into drug candidates, then tested for safety and effectiveness.

    "It takes time and a lot of persistence and focus," State says. "This [paper] is unlikely to lead to therapies tomorrow — but it lays an important foundation for them."

    Most human drugs are made to target proteins, Geschwind at UCLA says, so the newly published map of protein interactions offers an accessible entry point for pharmaceutical development.

    And researchers hope to combine recent technological advances in ways that accelerate that progress even more. "When you put together the ability to borrow from successes in other fields [such as cancer treatments], and the development of AI, we're at an inflection point that will hopefully shorten the time cycle," State says.

    Last week, Krogan's Quantitative Biosciences Institute received a $46 million grant from the Aligning Research to Impact Autism initiative, funded by philanthropist and Google co-founder Sergey Brin. The researchers are already working on next steps.

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