Autoimmune Disease

For applications in autoimmune (AI) diseases, our strategy has focused on antigen-specific modulation and pathway-specific modulation for controlling autoreactive T cell responses. Both approaches complement each other and offer unique opportunities for selective immune re-set of the dysfunctional compartment. The antigen-specific approach is pertinent to diseases with restricted or well-characterized autoantigens and deploys Immuno-STATs to directly modulate the autoreactive T cells. The pathway-specific approach exploits signals that can induce and sustain regulatory T cells, which can then control a broad population of autoreactive T cells. Hence, this approach may be more applicable to diseases with diverse unknown antigens. It is conceivable that the specific signals for Treg induction could be deployed in an Immuno-STAT framework for generation of antigen-specific Tregs.

Approaches to Modulate Autoreactive T Cell Responses

CUE-300 Series: Antigen-specific Approach

Our CUE-300 framework incorporates class II HLA alleles and is designed to target a broad range of addressable autoimmune diseases by selectively inhibiting the activity of autoreactive CD4+ T cells and/or enhancing the generation and functionality of regulatory T cells (Tregs). Selective targeting of the dysregulated axis in autoimmune diseases should avoid systemic immunosuppression and therefore should not hamper the immune system’s ability to effectively respond to malignancies and infectious organisms.

The CUE-300 Series Immuno-STATs focus on two general strategies:

  • Selective inhibition of autoreactive CD4+ T cells by delivering inhibitory signals; or
  • Selective expansion of antigen-specific CD4+ regulatory T cells (Tregs) to control aberrant activation of autoreactive T cells


Our lead candidate from the CUE-300 series is CUE-301, a Class II HLA DR0401-based Immuno-STAT that is designed to target and selectively inhibit proinsulin reactive CD4+ T cells in Type 1 diabetes to prevent these cells from injuring or killing insulin-producing beta cells in the pancreas.

CUE-301, contains two copies of the programmed death receptor ligand-1 (PD-L1) (an inhibitory Signal 2) and two copies of a pMHC (Signal 1) comprised of Class II MHC DRB1*0401 complexed with a peptide derived from proinsulin (amino acids 76 to 90), a prohormone precursor to insulin synthesized by beta cells of the islets of Langerhans of the pancreas. Proinsulin has been recognized as an important target antigen in Type 1 diabetes and prior studies have identified T cells from human patients that react against this epitope in the early stages of disease pathogenesis.

This program is a part of our collaboration with Merck & Co., Inc. where we have demonstrated that CUE-301 can selectively inhibit the expansion of proinsulin reactive T cells isolated from the blood of type 1 diabetes patients. In preclinical studies in DR0401-transgenic mice, CUE-301 was shown to inhibit the functional in vivo expansion of proinsulin-specific CD4+ T cells along with a notable reduction in production of pro-inflammatory cytokines.

Selective Suppression of Proins-specific T Cells In Vivo

Untreated Mice / IFNγ ELSIpot

IST Mice / IFNγ ELSIpot

Framework and Selective Suppression of Proins-specific T cells In Vitro

LEGEND: CUE-301 is Cue Biopharma’s first Immuno-STAT targeting an autoimmune disease, Type 1 diabetes. The CUE-300 series differs from the CUE-100 series in that the pMHC module is comprised Class II MHC with a DRB1*04 HLA allele and an immune checkpoint ligand, programmed death receptor-1 ligand (PD-L1), as the co-regulatory (or co-inhibitory) module.

Additional datasets underscoring our progress with CUE-301 were recently presented at an autoimmune meeting in January 2021. Download Poster

CUE-400 Series: Pathway-specific Approach

The CUE-400 series is focused on the generation of a novel bispecific molecule for differentiation and expansion of iTregs for applications in autoimmune diseases, graft versus host disease, or GVHD, and transplantrejection. The primary goals of developing the CUE-400 series of molecules is to harness signals that can generate large numbers of regulatory T cells, or Tregs, in the patient to control a broad repertoire of autoreactive and inflammatory T cells. This is especially important in controlling aberrant activation of autoreactive (or alloreactive) T cells in those conditions where the antigen(s) are unknown or involves multiple antigens, or in chronic stages of autoimmune diseases with extensive epitope spreading involving many different antigens. We believe that harnessing Tregs is an attractive opportunity for resetting immune balance and restoring functional tolerance.

Our focus has centered on expanding functional iTregs, which we believe offer untapped opportunities in autoimmune diseases and graft rejection. In contrast to IL-2-directed approaches aiming to expand the limited number and repertoire of nTregs, we believe induction and conversion of the pathogenic autoreactive T cells into iTreg may offer a more meaningful and lasting benefit to the patient. Harnessing structure-based rational protein engineering, we have generated the first molecule from our CUE-400 series, CUE-401, which is a novel IL-2-TGF-beta fusion protein. The structure of CUE-401 is shown below – it has one molecule of IL-2 fused to an Fc along with a masked TGF-beta molecule. Importantly, the IL-2 variant in CUE-401 has already demonstrated tolerability in the clinic since it is the same IL-2 variant that is present in our current clinical candidate CUE-101, albeit in a different valency (CUE-101 harbors 4 molecules of an affinity attenuated IL-2 along with bivalent tumor-peptide-HLA molecules to activate tumor-specific T cells).

CUE-401: Opportunity to Enhance Specificity and Selectivity

We have demonstrated that CUE-401 generated iTregs from conventional CD4+ T cells (as measured by robust induction of the master Treg transcription factor FoxP3). As shown below, we were able to generate iTregs from conventional CD4+ T cells from healthy subjects as well as from patients suffering from autoimmune diseases (RA -rheumatoid arthritis; IBD – inflammatory bowel disease). Importantly, in preclinical models, CUE-401 generated iTregs in equivalent or higher numbers when compared to the recombinant wild-type IL-2 and TGF-beta cytokines (“+recombinant cytokines”, as noted in the figure below). Functional assessments have confirmed that these iTregs can suppress T cell responses. Ongoing studies in preclinical models provide additional support for in vivo conversion of iTregs upon single-dose administration of CUE- 401.