Novel multi-disciplinary strategy to identify and target unconventional (neo)epitopes suitable for immunotherapy against colorectal cancer.

癌症患者中新表位的鉴定允许开发旨在靶向它们的免疫疗法。目前，在结直肠癌（CRC）中缺乏已知的可靶向表位。已经开发了预测算法，其旨在预测将在细胞表面呈递的抗原库。这包括预测蛋白酶体切割后产生的肽产物，这些产物与抗原呈递MHC-I分子的结合亲和力，以及MHC结合肽与T细胞受体（TCR）结合的预测因子。由于用于训练的高质量数据集数量不足，这些预测器目前缺乏准确性。 HLA-I分子和抗原之间的高度特异性相互作用由严格的基序要求决定，限制了许多抗原序列的结合。最近，蛋白酶体产生的剪接表位在免疫治疗中的潜力引起了人们的关注，因为可以由此产生的序列的理论组合开辟了一个未开发的潜在靶点库。然而，剪接肽呈递的频率仍然存在争议，估计范围为1- 34%。尽管如此，以前的工作，包括Mishto实验室的一些工作（1），已经证明蛋白酶体产生的剪接表位可以成为免疫治疗的靶点。其他非典型来源的表位，如非编码区的基因组最近已被调查，并提出作为免疫治疗的目标。 对免疫检查点抑制剂（ICI）治疗的反应与抗原特异性T细胞的活化和扩增有关。相关地，已经发现新抗原负荷与对ICI的应答相关，然而其本身不足以作为预测因子。事实上，Ciccarelli实验室进行的研究调查了从29名CRC患者队列中获得的数据，最近证明了突变克隆性在确定ICI反应方面的预测能力（2）。从该群组中，已经获得了TCR序列，其表明存在扩增的克隆。因此，研究它们的同源抗原与克隆性和对ICI疗法的应答的关系可能有助于鉴定联合疗法（过继性T细胞疗法+ ICI）的最佳靶标。此外，靶向共有或衍生自驱动突变的抗原呈现出有吸引力的治疗选择，因为它将能够开发广谱疗法，或者将靶向驱动癌细胞存活的蛋白质。

Identification of neoepitopes in cancer patient allows for the development of immunotherapies aimed at targeting them. Currently, there is a lack of known targetable epitope identified in colorectal cancer (CRC). Prediction algorithms have been developed that aim to predict the repertoire of antigens that will be presented at the cell surface. This includes prediction of peptide products generated following proteasomal cleavage, the binding affinity of those products to antigen-presenting MHC-I molecules, as well as predictors of MHC-bound peptide binding to T-cell receptors (TCR). These predictors currently suffer from lack of accuracy, due to insufficient amount of high-quality datasets for training. The highly specific interaction between HLA-I molecules and antigens dictated by stringent motif requirements restricts binding of many antigenic sequences. Recently the potential of proteasome-generated spliced epitopes in immunotherapies have garnered attention, as the theoretical combination of sequences that can be generated from this opens up an untapped pool of potential targets. However, the frequency of spliced peptide presentation remains a controversy, with estimates ranging from 1-34%. Nonetheless, previous works, including some in the Mishto lab (1), have demonstrated that proteasome-generated spliced epitopes could be targets for immunotherapies. Other noncanonical sources of epitopes such as non-coding regions of the genome have recently been investigated and proposed as immunotherapy targets. Response to therapy with immune checkpoint inhibitors (ICI) has been associated with activation and expansion of antigen-specific T-cells. Relatedly, the neoantigen burden has been found to correlate with response to ICI, however on its own is not sufficient as a predictor. Indeed, research conducted by the Ciccarelli lab investigating data obtained from a cohort of 29 CRC patients recently demonstrated the predictive power of mutational clonality in determining response to ICI (2). From this cohort, TCRsequences have been obtained, which indicated the presence of expanded clones. Hence investigating their cognate antigens, in relation to clonality and response to ICI therapy may aid in identifying optimal targets for combination therapy (adoptive T-cell therapy + ICI). Additionally, targeting of antigens that are shared or that derive from driver mutations present an attractive therapeutic option, given that it would enable the development of a broad-spectrum therapy, or would target a protein that drives cancer-cell survival, respectively.