Immune targets and neoantigens for cancer immunotherapy and precision medicine

Abstract

Harnessing the immune system to eradicate malignant cells is becoming a most powerful new approach to cancer therapy. FDA approval of the immunotherapy-based drugs, sipuleucel-T (Provenge), ipilimumab (Yervoy, anti-CTLA-4), and more recently, the programmed cell death (PD)-1 antibody (pembrolizumab, Keytruda), for the treatment of multiple types of cancer has greatly advanced research and clinical studies in the field of cancer immunotherapy. Furthermore, recent clinical trials, using NY-ESO-1-specific T cell receptor (TCR) or CD19-chimeric antigen receptor (CAR), have shown promising clinical results for patients with metastatic cancer. Current success of cancer immunotherapy is built upon the work of cancer antigens and co-inhibitory signaling molecules identified 20 years ago. Among the large numbers of target antigens, CD19 is the best target for CAR T cell therapy for blood cancer, but CAR-engineered T cell immunotherapy does not yet work in solid cancer. NY-ESO-1 is one of the best targets for TCR-based immunotherapy in solid cancer. Despite the great success of checkpoint blockade therapy, more than 50% of cancer patients fail to respond to blockade therapy. The advent of new technologies such as next-generation sequencing has enhanced our ability to search for new immune targets in onco-immunology and accelerated the development of immunotherapy with potentially broader coverage of cancer patients. In this review, we will discuss the recent progresses of cancer immunotherapy and novel strategies in the identification of new immune targets and mutation-derived antigens (neoantigens) for cancer immunotherapy and immunoprecision medicine.

Figure 1

Signaling and regulatory mechanisms of T cell activation and inhibition. T cell activation requires MHC/peptide-TCR stimulation (as signal 1) and co-stimulatory signaling between B7 and CD28 (as signal 2). Full activation of T cells is instructed by innate-immune signaling-induced cytokines (as signal 3). Meanwhile, T cell activation is regulated and suppressed by co-inhibitory signaling such as B7-CTLA-4 and PD-L1-PD-1 signaling, as well as by regulatory T cells.

Figure 2

T cell epitopes are generated from the primary and alternative open reading frames (ORFs) of mRNAs encoding tyrosinase-related protein 1 (TRP-1), NY-ESO-1, LAGE-1 and LAGE-1b.

Figure 3

Processing and presentation of MHC class I and II restricted antigens for CD8⁺ and CD4⁺ T cell recognition, respectively. (A) Endogenously expressed proteins are degraded through proteasomal degradation pathways to generate protein fragments, which are further trimmed and processed in ER to generate short (8-10 amino acids) peptides for loading onto MHC class I molecules. MHC-I/peptide complexes are transported to the cell surface for CD8⁺ T cell recognition. Exogenous proteins or peptides can also be processed and cross-presented for T cell recognition. (B) MHC class II α and β chains form a complex with the invariant chain (Ii) with a targeting sequence to MHC class II compartments (MIIC). The α/β/Ii complexes are transported to the MIIC, where Ii is processed and replaced with an antigenic peptide. Antigenic peptides can be generated from some endogenously expressed proteins with targeting sequence to the MIIC, or proteins targeted to autophagosomes through an autophagy-mediated pathway for protein degradation. Exogenous proteins are generally captured into early endosomes via endocytosis, and then further processed in the MIIC for loading onto MHC class II molecules. MHC-II/peptide complexes are finally transported to the cell surface and presented for recognition by CD4⁺ T cells.

Figure 4

Three types of mutations or alterations trigger CD4⁺ T cell responses. (A, B) Mutations in fibronectin (FN) and triosephosphate isomerase (TPI) directly constitute neoepitopes (neoantigens) for T cell recognition. (C) Mutations in CDC27 do not directly give rise to neoepitopes, but rather allow a nonmutated epitope to be processed and presented for T cell recognition. (D) Genetic alteration (chromosomal inversion) generates a fusion protein (LDLR-FUT), which gives rise to a neoepitope from the polypeptide translated from the FUT gene but in an antisense direction.

Figure 5

A schematic presentation of development of neoantigen-specific immunotherapy. Tumor samples and normal control tissues are obtained from a cancer patient for genomic DNA and RNA isolation. Whole-exome sequencing and bioinformatics analysis allows identification of non-synonymous mutations present in the tumor cells, but not in normal cells. RNA-seq will determine the expression profile of the mutated genes in cancer cells. Protein sequences with amino acid substitutions will be used to generate neoantigen-containing long peptides or tandem minigenes (TMGs), which are used to pulse autologous antigen presenting cells (APCs) in the form of peptides or transfected into autologous APCs or HLA-matched APCs. T cells obtained from the same patient will be used to screen against peptides-pulsed or TMGs-transfected APCs based on cytokine release from T cells or upregulation of activation makers (PD-1, 4-1BB and OX-40) on T cells after co-culture of T cells with APCs. Meanwhile, a single T cell can be isolated and tested for its reactivity against newly identified neoantigens. Neoantigen-specific T cells can be expanded for adoptive T cell therapy, as demonstrated for ERBB2IP (E805G) and KRAS (G12D)^,,, or used to identify neoantigen-specific T cell receptors (TCRs). These neoantigen-specific TCRs are cloned into expression vectors for further engineering of T cells in TCR-based immunotherapy. In addition, neoantigens can be used in synthetic (peptide, DNA and RNA) vaccines to elicit therapeutic immunity against cancer.