CAR-T Cell Therapy Moves Beyond Cancer to Autoimmune Diseases

It may sound like science fiction: removing a person’s immune cells, modifying them in a lab, and putting them back into the body to target the cells causing disease. But medical experts believe the approach, known as chimeric antigen receptor T-cell (CAR-T) therapy, could someday help treat a growing list of hard-to-manage conditions.

CAR-T cell therapy, a treatment that has transformed care for some people with leukemia and lymphoma, is now being studied in clinical trials for autoimmune diseases, including multiple sclerosis (MS), lupus, and scleroderma. Early results are encouraging, but the approach is still experimental. For now, it’s available for autoimmune diseases only through clinical trials, mainly for people whose disease hasn’t responded to standard treatments.

CAR-T therapy uses a patient’s own immune cells, called T cells, which are reengineered to find and destroy specific cells in the body.

What sets CAR-T therapy apart from most treatments is that it uses living cells that can keep working after they’re infused back into the body.

“CAR-T therapy is what we call a living drug,” says Michael Hurwitz, MD, PhD, a Yale Medicine medical oncologist and a team leader of the Cell Therapy Program at Yale Cancer Center. “When it works well, those cells don’t just attack their target once, they expand, persist, and continue functioning in the body.”

CAR-T therapy is typically given as a one-time treatment rather than an ongoing medication. Researchers are studying whether that single treatment could provide lasting benefit for people with autoimmune diseases.

Since 2017, the U.S. Food and Drug Administration (FDA) has approved seven CAR-T therapies, all for blood cancers. None is yet approved for an autoimmune disease.

The process generally involves these steps:

• Collecting cells: A patient’s T cells are collected through apheresis, an outpatient procedure that filters specific cells from the bloodstream.
• Engineering cells: In a lab, the T cells are genetically modified to recognize a specific target. In blood cancers, that target is on cancer cells. In autoimmune diseases, the target is on immune cells that drive the disease.
• Multiplying cells: The modified cells are grown over several weeks until there are enough for treatment.
• Preparing the body: Patients usually receive a short course of chemotherapy to prevent the immune system from blocking the T cells that are infused, and to make space for the new cells to grow.
• Infusing cells: The CAR-T cells are infused back into the patient through a vein, where they seek out and destroy cells carrying their target.

In an autoimmune disease, the immune system mistakenly attacks the body’s own healthy tissues.

“Many autoimmune diseases are caused by the immune system going rogue,” says Dr. Hurwitz, who is also an associate professor of internal medicine at Yale School of Medicine (YSM). “If you can identify and eliminate the cells responsible, you may be able to reset the disease rather than simply suppress it.”

Most current autoimmune treatments work by calming or suppressing the immune system, and many must be taken long-term. Researchers are studying whether CAR-T can instead remove the specific immune cells driving the disease, potentially leading to longer-lasting control.

At Yale Cancer Center, specialists in hematology–oncology, rheumatology, and neurology are working together to study CAR-T therapy for MS, scleroderma, and lupus in clinical trials. The program began in August 2025, when the first patient with MS received CAR-T cells. Yale clinicians were also the first in the state of Connecticut to perform the first CAR-T infusion for lupus.

MS is a disease in which the immune system attacks the brain and spinal cord. Many of today’s most effective MS treatments target B cells, a type of immune cell that helps drive inflammation. But those therapies don’t always stop the disease from progressing.

Researchers are studying whether CAR-T therapy can eliminate disease-causing B cells more thoroughly, including cells that have settled in tissues rather than circulating in the blood.

“The monoclonal antibodies we use now do a very good job of clearing B cells from the blood, but they don’t effectively deplete B cells that are in tissues, and they don’t go into the brain,” says Erin Longbrake, MD, PhD, a Yale Medicine neurologist. (Monoclonal antibodies are lab-made proteins designed to target specific cells.) “A CAR-T cell doesn’t have those barriers.”

The approach remains experimental, and current studies include only people with the most treatment-resistant MS.

“The big questions now are whether this actually changes the course of the disease, and in which patients,” says Dr. Longbrake, who is also an associate professor of neurology at YSM. “These are very small numbers, but so far, the safety profile has been encouraging. Still, we need to understand who this might help—and who it won’t.”

Lupus (systemic lupus erythematosus) is an autoimmune disease that can cause inflammation in the joints, skin, kidneys, and other organs.

Researchers are studying whether CAR-T therapy can eliminate the immune cells that drive lupus and whether this “immune reset” can lead to lasting benefits. In small early studies, some people with severe lupus have gone into remission and been able to stop their other lupus medications. Larger clinical trials are needed to learn how long those responses last and who is most likely to benefit.

Scleroderma, also called systemic sclerosis, is an autoimmune disease that can cause inflammation and scarring (fibrosis) in the skin and internal organs, particularly the lungs.

Current treatments can slow the disease but do little to restore function once scarring has developed, says Monique Hinchcliff, MD, MS, director of the Yale Scleroderma Program and associate professor of medicine at YSM. Researchers are studying whether CAR-T therapy could do more.

“If we can put you on medicines that just maintain your lung function where you are, that’s a win,” Dr. Hinchcliff says. “But wouldn’t it be great if we could go beyond that and prevent lung function decline in patients with systemic sclerosis at high risk for progressive lung disease?”

CAR-T therapy can trigger strong immune reactions. Known side effects, mostly studied in people with cancer, include:

• Cytokine release syndrome (CRS), a widespread inflammatory reaction that can cause high fever, low blood pressure, and difficulty breathing. In severe cases, it can lead to kidney failure and can be life-threatening.
• Neurologic side effects, such as confusion, trouble speaking, or, less commonly, seizures
• Low blood counts and a higher risk of infection, particularly in the weeks after treatment

In cancer patients, these reactions tend to be more severe when there’s more cancer in the body, says Stuart Seropian, MD, director of Yale Cancer Center’s Stem Cell Transplant Program and a professor of internal medicine at YSM.

“In autoimmune disease, that burden just isn’t there in the same way,” he says, which is one reason side effects so far have appeared more manageable in people with autoimmune diseases. Researchers are still gathering data on safety, including long-term effects.

Because of these risks, CAR-T must be given by specially trained teams that can monitor patients closely and manage side effects quickly.

“It requires a program, not just a physician, to administer these treatments,” Dr. Seropian says.

“These are extraordinary therapies,” Dr. Hurwitz says. “But they require us to be very intentional—about who we treat, where we treat, and what risks patients are willing to accept.”

For now, CAR-T therapy for autoimmune diseases is available only through clinical trials. Most trials enroll people whose disease is severe or hasn’t responded to several standard treatments. Each trial has its own eligibility criteria.

If you have MS, lupus, or scleroderma and are curious about CAR-T therapy:

• Talk with your specialist. Your neurologist or rheumatologist can help you understand whether a trial might be appropriate and how it compares with your current options.
• Don’t change your current treatment on your own. Approved therapies remain the standard of care and help many people manage their disease well.
• Ask about clinical trials. You can search for clinical trials at Yale School of Medicine or ask your doctor about trials that are available for you to participate in.

It’s still too early to know exactly what role CAR-T therapy will play in treating autoimmune disease. Over the next several years, larger clinical trials will help answer key questions: how long the benefits last, which patients are most likely to respond, and how safe the treatment is over the long term.

Researchers hope CAR-T could eventually offer a new option for people whose disease remains difficult to control with existing treatments.