CAR-based cell therapy for autoimmune diseases

Abstract

Chimeric antigen receptor (CAR)-based cell therapies, initially designed for oncology, are rapidly advancing as a novel and highly targeted approach for the treatment of autoimmune diseases (AIDs). By harnessing engineered immune cells to eliminate autoreactive immune components or restore immune homeostasis, CAR-based strategies offer new avenues beyond conventional immunosuppression. In this review, we summarize current applications of CAR-T cells in autoimmune diseases, and discuss emerging approaches including CAR-Tregs, chimeric autoantibody receptor T (CAAR-T) cells, CAR-NK cells, and CAR-macrophages. We also describe advances in CAR design, including antigen selection, co-stimulatory domains, and safety control mechanisms, which are critical for improving therapeutic precision and reducing side effects. In addition, we highlight the role of synthetic biology in enabling more flexible and controllable CAR functions. Finally, we discuss the main challenges facing clinical translation, such as antigen specificity, long-term persistence, and manufacturing feasibility. These developments collectively support the potential of CAR-based therapies as a next-generation option for autoimmune disease treatment.

Keywords: CAR-T cell; autoimmune disease; cell therapy; chimeric antigen receptor; synthetic biology.

Figure 1

Mechanisms of target cell apoptosis induced by CAR-T cells. CAR-T cells eliminate target cells through two primary apoptotic pathways. One involves the secretion of perforin to create pores in the target cell membrane, allowing granzyme B to enter and activate caspase cascades. The second mechanism involves FasL expression on CAR-T cells, which engages Fas on target cells, triggering Caspase-dependent apoptotic signaling. The illustrated CAR construct contains a scFv targeting CD19, a co-stimulatory domain (e.g., CD28 or 4-1BB), and a T cell activation domain (CD3ζ). FasL, Fas ligand; scFv, single-chain variable fragment; CAR, chimeric antigen receptor.

Figure 2

Strategies for CAR-T cell generation: in vitro engineering and in vivo delivery. (A) Ex vivo generation of CAR-T cells: T cells are isolated from peripheral blood and activated using CD3/CD28 stimulation. CAR genes are introduced via lentiviral transduction. The engineered CAR-T cells are then expanded in vitro and infused back into the patient. CAR: chimeric antigen receptor. (B) In vivo delivery of CAR constructs: engineered eVLPs carrying RNP (comprised Cas9 protein, crRNA and tracrRNA) and HA-CAR, or targeted virus carrying Cas9 mRNA, gRNAs, and HA-CAR are administered to directly transduce T cells in vivo, bypassing the need of lymphodepletion. eVLPs: engineered virus-like particles; RNP: ribonucleoprotein; HA-CAR: homology arms-flanking CAR sequence. (C) CRISPR-mediated targeted insertion of CAR into the TRAC locus: guide RNAs (gRNAs) and HA-CAR are used to disrupt the endogenous TCR and insert the CAR gene into the first exon of TCR α constant (TRAC) gene, reducing risks of graft-versus-host disease in allogeneic settings. RNP, ribonucleoprotein; TRAV, T cell receptor alpha variable region gene; TRAJ, T cell receptor alpha joining region gene; TRAC, T cell receptor alpha constant region gene; SA, splice acceptor; P2A, 2A peptide; PA, poly-A tail; LHA, left homology arm; RHA, right homology arm; eVLPs, Engineered virus-like particles.

Figure 3

Controllable CAR-T cells with inducible safety switches. (A) Drug-inducible suicide switch: The iCasp-9 system is integrated into CAR-T cells. Upon administration of Rimiducid, iCasp-9 dimerizes and activates downstream caspase signaling, leading to CAR-T cell apoptosis and rapid termination of activity. iCasp-9: inducible caspase-9. (B) Drug-inducible activation switch: The CAR structure is split with FKBP12 and FRB domains, which can be dimerized in the presence of Rapamycin. This interaction restores CAR signaling, thereby enabling CAR-T cells activation in a ligand-dependent manner.

Figure 4

Engineered CAR-T cells and CAR-Tregs for autoimmune disease treatment. (A) Transient CAR-T cells are generated by delivering LNP or tLNP-encapsulated CAR mRNA targeting CD19 into T cells. Unlike conventional CAR-T cells, CAR expression here is transient and does not integrate into genomic DNA. LNP: lipid nanoparticle; tLNP: targeted lipid nanoparticle. (B) Schematic of tLNP-mediated CAR mRNA delivery: anti-CD4-targeted lipid nanoparticles encapsulating nucleoside-modified CAR mRNA (uridine replaced by 1-methylpseudouridine, m¹Ψ) are internalized by T cells through endocytosis, resulting in transient CAR expression. (C) CAAR-T cells are engineered to express autoantigen peptides in their extracellular domains, enabling selective targeting and depletion of autoantibody-producing cells via BCR engagement. CAAR: Chimeric autoantibody receptor; BCR: B-cell receptor. (D) CAR-Treg cells are engineered through FoxP3 overexpression or stabilization via TSDR demethylation in CD4⁺ T cells expressing tissue-specific CAR, thereby inducing a Treg-like phenotype. Upon antigen recognition, these CAR-Treg cells exert immunosuppressive functions, primarily by secreting IL-10 and TGF-β. FoxP3: Forkhead box P3; TSDR: Treg-specific demethylated region; CAR: chimeric antigen receptor; IL-2R: interleukin-2 receptor.

Figure 5

Logic-gated CAR-T cells for precise targeting of autoreactive cells. (A) “OR” gate design: CAR-T cells express tandem CARs recognizing CD19 and BCMA. Binding to either antigen (on B-cells or plasma cells, respectively) is sufficient to activate the cell, expanding the therapeutic coverage. (B) “AND” gate design: Two separate CARs are engineered with distinct intracellular signaling domains. Full activation occurs only when both BCMA and autoantigen-specific BCR are engaged on the same target cell, enabling selective elimination of pathogenic autoantibody-producing cells while sparing non-pathogenic counterparts. CAR, chimeric antigen receptor; BCR, B-cell receptor.

Figure 6

SynNotch-regulated CAR-NK cells for conditional IL-15 expression. (A) Conventional CAR-NK cells constitutively express IL-15 to promote NK cell survival, proliferation, and cytotoxic function. However, continuous IL-15 expression can induce off-target toxicity due to the undesired activation of host NK cells. (B) SynNotch CAR-NK cells use scFv-A to recognize antigen A and mediate cytotoxicity, while scFv-B detects antigen B to activate the SynNotch pathway. Upon antigen B binding, a transcription factor is released to induce IL-15 expression. Once antigen B is no longer present, IL-15 production stops, thereby enhancing safety by limiting cytokine release to dual-antigen recognition. scFv, single-chain variable fragment.