Stem Cell Therapy for Autoimmune Disease
Stem cells have the unique ability to turn into any cell type when given specific stimuli. Recently, they have become a promising avenue for autoimmune disease treatment. “They are like a blank slate,” says Juan Domínguez-Bendala, Director of Stem Cell & Pancreatic Regeneration at the Diabetes Research Institute, University of Miami Miller School of Medicine.
“They are waiting for instructions to become one thing or another, and it’s up to us to tell them what path to take.”
What are the Different Types of Stem Cells?
Stem cells fall into different categories based on their source and what type of cell they can become:
- Embryonic stem cells, derived from early-stage embryos, can become any cell type.
- Adult stem cells are found in different tissues in the body. They can give rise to different cell types but are much more limited in what they can become. For example, hematopoietic stem cells (HSCs) are found in the bone marrow and can become different types of blood cells and immune cells. Adult stem cells are meant to regenerate damaged tissues and cells.
- Induced pluripotent stem cells are differentiated cells that are genetically programmed back to embryonic stem cells so that they can be later differentiated into any cell type.
Where has Stem Cell Therapy Shown Promise in Treating Autoimmune Disease?
“In general, for cell therapy in autoimmune diseases, there are two approaches,” says Saad Kenderian, Professor of Medicine, Immunology, and Oncology at Mayo Clinic. “Either you kill the cells that cause autoimmune diseases or you use suppressive cells and engineer them to go to the site of the inflammation.”
Hematopoietic stem cell transplantation (HSCT) “resets” the immune system
The idea behind stem cell transplantation is that the technique removes a patient’s self-reactive immune system and replaces it with a self-tolerant immune system. This process either uses hematopoietic stem cells from a donor (allogenic) or from the patient (autologous). The patient undergoes chemotherapy to delete the immune system. The stem cells are placed into the patient where they travel to the bone marrow, where they create new blood cells and regenerate a new, self-tolerant immune system. In contrast to allogeneic stem cell transplantation, autologous stem cell transplants require extracting a patient’s stem cells from the bone marrow using medication and collecting them from the blood (1). Autologous transplants do not have the incompatibility issue that donor stem cells may have.
This technique is most often used to treat cancers like lymphomas and myeloma, but has applications in treating autoimmune diseases. As of 2020, about 3,000 patients with autoimmune diseases have been treated with HSCT (2). According to the American Society for Blood and Marrow Transplantation, HSCT should be the “standard of care, clinical evidence available” for multiple sclerosis (MS) patients with treatment-refractory relapsing MS (3). But there are many risks associated with HSCTs since it removes your existing immune system and there’s the potential for your body to reject the transplanted cells. “You don’t do a bone marrow transplant unless your life depends on it,” says Domínguez-Bendala.
Dampening inflammation and promoting immune tolerance
One type of stem cell, the mesenchymal stromal cells (MSCs), have a unique characteristic: they’re immunosuppressive and regenerative. Mesenchymal stromal cells (MSC) can be isolated from many tissue types in the body. In the body, they migrate to damaged tissues and can inhibit the growth and function of T cells and regulate expression of inflammatory molecules (4). “MSCs have been quite safe,” says Kenderian. “They have been widely used in the treatment of autoimmune diseases, but their activity has been kind of modest. You see some activity in some patients and no activity in others.”
A recent study from Kenderian’s team reported the engineering of MSCs with chimeric antigen receptors (the technology used in CAR-T therapy) (5). “We could engineer the receptor in a way to get it to [target] different autoimmune diseases,” says Kenderian. He found that these cells were site specific and induced immunosuppression at the desired location.
“We’re looking forward to translating this into a phase one clinical trial, and also see this as a platform that can be modified to make MSCs more suppressive in different diseases,” says Kenderian. “I think it’s a platform that can be engineered and adapted to develop designer therapy for a specific disease.”
Applications for type 1 diabetes
Type 1 diabetes has been long treated by giving the body insulin. In recent years, scientists have attempted to replenish insulin-producing cells, or islets, that have been destroyed by autoimmune attacks. Transplanting islet cells from donors has been difficult because organ donations are limited, which is why the field has turned to stem cells. When stem cells are transformed into a type of islet cell called beta cells, they offer a supply of insulin when placed into the body. However, the challenge then becomes keeping the patient’s immune system from attacking these cells. Many strategies to shield these cells from the immune system have reached clinical trials (6).
“When you think about a cure for type one diabetes, it entails two things. One of them is to replenish cells that have been lost. The other is to correct autoimmunity, which is what caused the disease in the first place,” says Domínguez-Bendala.
“Ultimately, if you can have your own body reheal your pancreas, and regrow your own cells, as opposed to having to transplant them, I think it will be much more holistic and the way to a cure,” says Domínguez-Bendala.
What are the Potential Risks and Side Effects Associated with Stem Cell Treatments?
(1) Reduced ability to fight infections: Many of the potential infection risks associated with bone marrow transplantation occur in the time between deleting self-reacting immune cells and the formation of a new immune system. Infections, that would otherwise be minor illnesses, could become life-threatening as the body doesn’t have a way to fight them off.
(2) Low blood counts: For bone marrow transplants, low blood counts occur before the stem cells migrate to the bone marrow where they make new blood cells. There can be an increased bleeding risk as platelets (which affect clotting) are low after stem cell transplant.
(3) Tumor formation: “The very reason that makes stem cells appealing, which is the fact that they proliferate all the time so you can get unlimited numbers of them, is also a reason for concern,” says Domínguez-Bendala. Because stem cells live so long and divide rapidly, they have the potential to acquire mutations that lead them to form tumors. Scientists, like Domínguez-Bendala, are working on mechanisms to prevent uncontrolled growth from stem cells (7).
(4) Graft versus host disease: For transplanted stem cells that did not originate from the patient, it’s possible that the body recognizes donated stem cells as foreign and attacks them.
Ongoing Clinical Trials Investigating Stem Cell Therapy for Autoimmune Disease
The following clinical trials are now recruiting or will be recruiting (*as of publication date September 25, 2025):
- Autologous Hematopoietic Stem Cell Transplantation for Refractory Multiple Sclerosis
- Best Available Therapy Versus Autologous Hematopoetic Stem Cell Transplant for Multiple Sclerosis (BEAT-MS) (BEAT-MS)
- Evaluate the Safety and Efficacy of Allogeneic Umbilical Cord Mesenchymal Stem Cells in Patients With Multiple Sclerosis (UMSC01)
- Observational Study in Multiple Sclerosis Patients Treated With Autologous Hematopoietic Stem Cell Transplantation (OMST)
See all ongoing and not-yet-recruiting clinical trials using stem cells to treat autoimmune diseases here.
About the Author
A microbiologist turned freelance science writer who works with life science companies, nonprofits, and academic institutions on anything from news stories, explainer articles, and content marketing. She shares the wonderful world of microbes on her blog The Microbial Menagerie.
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Cohen, J. A., et al (2019). Autologous Hematopoietic Cell Transplantation for Treatment-Refractory Relapsing Multiple Sclerosis: Position Statement from the American Society for Blood and Marrow Transplantation. Biology of blood and marrow transplantation. Journal of the American Society for Blood and Marrow Transplantation, 25(5), 845–854.
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Sirpilla, O., et al. Mesenchymal stromal cells with chimaeric antigen receptors for enhanced immunosuppression. Nat. Biomed. Eng, 8, 443–460 (2024).
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