Personalized immunotherapy in cancer precision medicine

With the significant advances in cancer genomics using next-generation sequencing technologies, genomic and molecular profiling-based precision medicine is used as a part of routine clinical test for guiding and selecting the most appropriate treatments for individual cancer patients. Although many molecular-targeted therapies for a number of actionable genomic alterations have been developed, the clinical application of such information is still limited to a small proportion of cancer patients. In this review, we summarize the current status of personalized drug selection based on genomic and molecular profiling and highlight the challenges how we can further utilize the individual genomic information. Cancer immunotherapies, including immune checkpoint inhibitors, would be one of the potential approaches to apply the results of genomic sequencing most effectively. Highly cancer-specific antigens derived from somatic mutations, the so-called neoantigens, occurring in individual cancers have been in focus recently. Cancer immunotherapies, which target neoantigens, could lead to a precise treatment for cancer patients, despite the challenge in accurately predicting neoantigens that can induce cytotoxic T cells in individual patients. Precise prediction of neoantigens should accelerate the development of personalized immunotherapy including cancer vaccines and T-cell receptor-engineered T-cell therapy for a broader range of cancer patients.     

Transformation of Old Concepts for a New Era of Cancer Immunotherapy: Cytokine Therapy and Cancer Vaccines as Combination Partners of PD1/PD-L1 Inhibitors

Purpose of Review

Immune checkpoint inhibitors (ICI) are only effective in a subset of patients. Here, we will review the rationale and data supporting the combination of PD-1 pathway inhibition with recombinant cytokines and neoantigen-based cancer vaccines that can potentially increase the number of patients who will benefit from immunotherapy.

Recent Findings

The safety and tolerability of new interleukin(IL)-2 formulations, IL-15 super agonist, and PEGylated IL-10 have been evaluated in early phase clinical trials with promising efficacy data, both as monotherapy and in combination with ICI. Larger studies focusing on the efficacy of these combinations are ongoing. Personalized neoantigen-based cancer vaccines, enabled by improvements in sequencing computational capabilities, have been proven to be feasible, safe, and able to trigger a consistent vaccine-specific immune response in cancer patients.

Summary

New pharmacologically modified recombinant cytokines and personalized neoantigen-based vaccines may turn these approaches into powerful tools for effective combination immunotherapy.

     

Tumour neoantigen mimicry by microbial species in cancer immunotherapy

Tumour neoantigens arising from cancer-specific mutations generate a molecular fingerprint that has a definite specificity for cancer. Although this fingerprint perfectly discriminates cancer from healthy somatic and germline cells, and is therefore therapeutically exploitable using immune checkpoint blockade, gut and extra-gut microbial species can independently produce epitopes that resemble tumour neoantigens as part of their natural gene expression programmes. Such tumour molecular mimicry is likely not only to influence the quality and strength of the body’s anti-cancer immune response, but could also explain why certain patients show favourable long-term responses to immune checkpoint blockade while others do not benefit at all from this treatment. This article outlines the requirement for tumour neoantigens in successful cancer immunotherapy and draws attention to the emerging role of microbiome-mediated tumour neoantigen mimicry in determining checkpoint immunotherapy outcome, with far-reaching implications for the future of cancer immunotherapy.Subject terms: Tumour immunology, Tumour immunology     

肿瘤的免疫吸引作用

虽然肿瘤是免疫逃逸的结果,但肿瘤中也经常发现肿瘤相关性嗜酸性粒细胞、中性粒细胞和各种免疫细胞,这些免疫细胞可以攻击肿瘤.肿瘤吸引免疫细胞主要通过肿瘤新抗原、肿瘤体、肿瘤外泌体和肿瘤细胞死亡等方式来实现.理解肿瘤免疫吸引作用可以改变肿瘤免疫治疗策略,强调免疫治疗联合放化疗的重要性.     

精准细胞免疫治疗中肿瘤新抗原相关研究进展

如何通过细胞表面抗原使免疫系统区分正常细胞和癌细胞是肿瘤细胞免疫治疗的关键。最新的技术使人们了解到,由于肿瘤细胞突变产生新的表位肽,继而引起患者的特异性免疫应答;并且最新研究表明,这种肿瘤新抗原（neoantigens）的识别将成为临床免疫治疗的重要突破点。相关结果表明,在癌症免疫治疗中,肿瘤新抗原可以作为一种生物标志物,开发并增强针对这类抗原选择性T细胞的反应性,为新型免疫治疗带来希望。精准细胞免疫治疗(precision cell immunotherapy treatment,PCIT)是通过高通量基因测序及大数据分析,获得针对癌细胞特异性新型抗原和高效应的精准T细胞(precision T cell for neoantigen,PNA-T),进而富集 PNA-T对肿瘤患者进行精准细胞免疫治疗。     

Advances in personalized cancer immunotherapy

There are currently three major approaches to T cell-based cancer immunotherapy, namely, active vaccination, adoptive cell transfer therapy and immune checkpoint blockade. Recently, this latter approach has demonstrated remarkable clinical benefits, putting cancer immunotherapy under the spotlight. Better understanding of the dynamics of anti-tumor immune responses (the “Cancer-Immunity Cycle”) is crucial for the further development of this form of treatment. Tumors employ multiple strategies to escape from anti-tumor immunity, some of which result from the selection of cancer cells with immunosuppressive activity by the process of cancer immunoediting. Apart from this selective process, anti-tumor immune responses can also be inhibited in multiple different ways which vary from patient to patient. This implies that cancer immunotherapy must be personalized to (1) identify the rate-limiting steps in any given patient, (2) identify and combine strategies to overcome these hurdles, and (3) proceed with the next round of the “Cancer-Immunity Cycle”. Cancer cells have genetic alterations which can provide the immune system with targets by which to recognize and eradicate the tumor. Mutated proteins expressed exclusively in cancer cells and recognizable by the immune system are known as neoantigens. The development of next-generation sequencing technology has made it possible to determine the genetic landscape of human cancer and facilitated the utilization of genomic information to identify such candidate neoantigens in individual cancers. Future immunotherapies will need to be personalized in terms of the identification of both patient-specific immunosuppressive mechanisms and target neoantigens.     

Nanomaterial-based delivery vehicles for therapeutic cancer vaccine development

Nanomaterial-based delivery vehicles such as lipid-based, polymer-based, inorganics-based, and bio-inspired vehicles often carry distinct and attractive advantages in the development of therapeutic cancer vaccines. Based on various delivery vehicles, specifically designed nanomaterials-based vaccines are highly advantageous in boosting therapeutic and prophylactic antitumor immunities. Specifically, therapeutic vaccines featuring unique properties have made major contributions to the enhancement of antigen immunogenicity, encapsulation efficiency, biocompatibility, and stability, as well as promoting antigen cross-presentation and specific CD8⁺ T cell responses. However, for clinical applications, tumor-associated antigen-derived vaccines could be an obstacle, involving immune tolerance and deficiency of tumor specificities, in achieving maximum therapeutic indices. However, when using bioinformatics predictions with emerging innovations of in silico tools, neoantigen-based therapeutic vaccines might become potent personalized vaccines for tumor treatments. In this review, we summarize the development of preclinical therapeutic cancer vaccines and the advancements of nanomaterial-based delivery vehicles for cancer immunotherapies, which provide the basis for a personalized vaccine delivery platform. Moreover, we review the existing challenges and future perspectives of nanomaterial-based personalized vaccines for novel tumor immunotherapies.     

Neoantigen vaccine: An emerging immunotherapy for hepatocellular carcinoma

Tumor-specific neoantigens, which are expressed on tumor cells, can induce an effective antitumor cytotoxic T-cell response and mediate tumor regression. Among tumor immunotherapies, neoantigen vaccines are in early human clinical trials and have demonstrated substantial efficiency. Compared with more neoantigens in melanoma, the paucity and inefficient identification of effective neoantigens in hepatocellular carcinoma (HCC) remain enormous challenges in effectively treating this malignancy. In this review, we highlight the current development of HCC neoantigens in its generation, screening, and identification. We also discuss the possibility that there are more effective neoantigens in hepatitis B virus (HBV)-related HCC than in non-HBV-related HCC. In addition, since HCC is an immunosuppressive tumor, strategies that reverse immunosuppression and enhance the immune response should be considered for the practical exploitation of HCC neoantigens. In summary, this review offers some strategies to solve existing problems in HCC neoantigen research and provide further insights for immunotherapy.     

Measurement of tumor mutational burden (TMB) in routine molecular diagnostics: in silico and real-life analysis of three larger gene panels

Assessment of Tumor Mutational Burden (TMB) for response stratification of cancer patients treated with immune checkpoint inhibitors is emerging as a new biomarker. Commonly defined as the total number of exonic somatic mutations, TMB approximates the amount of neoantigens that potentially are recognized by the immune system. While whole exome sequencing (WES) is an unbiased approach to quantify TMB, implementation in diagnostics is hampered by tissue availability as well as time and cost constrains. Conversely, panel-based targeted sequencing is nowadays widely used in routine molecular diagnostics, but only very limited data are available on its performance for TMB estimation. Here, we evaluated three commercially available larger gene panels with covered genomic regions of 0.39 Megabase pairs (Mbp), 0.53 Mbp and 1.7 Mbp using i) in silico analysis of TCGA (The Cancer Genome Atlas) data and ii) wet-lab sequencing of a total of 92 formalin-fixed and paraffin-embedded (FFPE) cancer samples grouped in three independent cohorts (non-small cell lung cancer, NSCLC; colorectal cancer, CRC; and mixed cancer types) for which matching WES data were available. We observed a strong correlation of the panel data with WES mutation counts especially for the gene panel >1Mbp. Sensitivity and specificity related to TMB cutpoints for checkpoint inhibitor response in NSCLC determined by wet-lab experiments well reflected the in silico data. Additionally, we highlight potential pitfalls in bioinformatics pipelines and provide recommendations for variant filtering. In summary, our study is a valuable data source for researchers working in the field of immuno-oncology as well as for diagnostic laboratories planning TMB testing.     

放疗对肿瘤微环境的重塑及增强免疫治疗疗效机制的研究进展

以免疫检查点抑制剂(ICIs)为主的免疫治疗改变了传统癌症治疗手段,但对于大多数类型的癌症,ICIs治疗受益十分有限(10％～30％),并且在某些癌症类型中基本无效(如胰腺癌、脑胶质瘤).将ICIs治疗与现有及潜在的疗法相结合从而克服肿瘤原发性和获得性抵抗,对于提高治疗率、增加疗效的持久性和延长患者的生存期有重要意义....     

个体化新抗原特异性T细胞过继免疫：任重道远，砥砺前行

近年来,肿瘤新抗原掀开了个体化免疫治疗的新篇章,作为基于新抗原个体化免疫治疗的重要组成部分,新抗原特异 性T细胞的过继输注（ACT）疗法备受瞩目。本文将首先从新抗原特异性T细胞ACT治疗应用策略及临床应用现状介绍新抗原 特异性T细胞ACT治疗这一新兴的精准免疫治疗的发展现状,然后从新抗原的预测、新抗原特异性T细胞筛选及扩增等方面系 统地总结新抗原T细胞ACT治疗所面临的阻碍和挑战,最后从优化新抗原预测、增加新抗原特异性T细胞数量和多样性、防止新 抗原特异性T细胞过度分化或死亡、缩短生产周期和减少生产成本及探索联合治疗方式等五个方面对该领域的未来发展机遇和 研究方向进行重点阐述。     

Residue substitution enhances the immunogenicity of neoepitopes from gastric cancers

Objective:Neoantigens arising from gene mutations in tumors can induce specific immune responses, and neoantigen-based immunotherapies have been tested in clinical trials. Here, we characterized the efficacy of altered neoepitopes in improving immunogenicity against gastric cancer.Methods:Raw data of whole-exome sequencing derived from a patient with gastric cancer were analyzed using bioinformatics methods to identify neoepitopes. Neoepitopes were modified by P1Y (the first amino acid was replaced by tyrosine) and P2L (the second amino acid was replaced by leucine). T2 binding and stability assays were used to detect the affinities between the neoepitopes and the HLA molecules, as well as the stabilities of complexes. Dendritic cells (DCs) presented with neoepitopes stimulated naïve CD8⁺ T cells to induce specific cytotoxic T lymphocytes. ELISA and carboxyfluorescein succinimidyl ester were used to detect IFN-γ and TNF-α levels, and T cell proliferation. Perforin was detected by flow cytometry. The cytotoxicity of T cells was determined using the lactate dehydrogenase assay.Results:Bioinformatics analysis, T2 binding, and stability assays indicated that residue substitution increased the affinity between neoepitopes and HLA molecules, as well as the stabilities of complexes. DCs presented with altered neoepitopes stimulated CD8⁺T cells to release more IFN-γ and had a greater effect on promoting proliferation than wild-type neoepitopes. CD8⁺T cells stimulated with altered neoepitopes killed more wild-type neoepitope-pulsed T2 cells than those stimulated with wild-type neoepitopes, by secreting more IFN-γ, TNF-α, and perforin.Conclusions:Altered neoepitopes exhibited greater immunogenicity than wild-type neoepitopes. Residue substitution could be used as a new strategy for immunotherapy to target neoantigens.     

Personalized cancer vaccination in head and neck cancer

Cancer is characterized by an accumulation of somatic mutations that represent a source of neoantigens for targeting by antigen-specific T cells. Head and neck squamous cell carcinoma (HNSCC) has a relatively high mutation burden across all cancer types, and cellular immunity to neoantigens likely plays a key role in HNSCC clinical outcomes. Immune checkpoint inhibitors (CPIs) have brought new treatment options and hopes to patients with recurrent and/or metastatic HNSCC. However, many patients do not benefit from CPI therapies, highlighting the need for novel immunotherapy or combinatorial strategies. One such approach is personalized cancer vaccination targeting tumor-associated antigens and tumor-specific antigens, either as single agents or in combination with other therapies. Recent advances in next-generation genomic sequencing technologies and computational algorithms have enabled efficient identification of somatic mutation-derived neoantigens and are anticipated to facilitate the development of cancer vaccine strategies. Here, we review cancer vaccine approaches against HNSCC, including fundamental mechanisms of a cancer vaccine, considerations for selecting appropriate antigens, and combination therapies.     

放疗联合免疫治疗癌症的研究进展

放疗不仅是肿瘤局部治疗的重要手段,同时也对免疫功能有重要的调节作用。放疗可通过产生新抗原、调节细胞因子释放、提高肿瘤对免疫细胞杀伤作用敏感性等方式调节机体抗肿瘤免疫应答。近年来部分研究和临床实践发现,放疗联合免疫治疗在部分病例中出现“远位效应”,照射野范围外的转移性病灶有部分或完全缓解,显示放疗联合免疫治疗的良好前景;但相关机制以及放疗剂量、分割方式等因素对免疫的影响仍有待进一步研究。本文综述了放疗影响免疫的机制以及放疗联合免疫治疗的研究进展。     

Genomic and neoantigen evolution from primary tumor to first metastases in head and neck squamous cell carcinoma

Head and neck cell squamous-cell carcinomas (HNSCC) are a group of common cancers typically associated with tobacco use and human papilloma virus infection. Up to half of all cases will suffer a recurrence after primary treatment. As such, new therapies are needed, including therapies which promote the anti-tumor immune response. Prior work has characterized changes in the mutation burden between primary and recurrent tumors; however, little work has characterized the changes in neoantigen evolution. We characterized genomic and neoantigen changes between 23 paired primary and recurrent HNSCC tumors. Twenty-three biopsies from patients originally diagnosed with locally advanced disease were identified from the Washington University tumor bank. Whole exosome sequencing, RNA-seq, and immunohistochemistry was performed on the primary and recurrent tumors. Within these tumors, we identified 6 genes which have predicted neoantigens in 4 or more patients. Interestingly, patients with neoantigens in these shared genes had increased CD3+ CD8+ T cell infiltration and duration of survival with disease. Within HNSCC tumors examined here, there are neoantigens in shared genes by a subset of patients. The presence of neoantigens in these shared genes may promote an anti-tumor immune response which controls tumor progression.     

Targeting immunosupportive cancer therapies: accentuate the positive, eliminate the negative

In this Commentary we aim to provide an overview of some specific examples of cancer therapeutics, including targeted approaches using monoclonal antibodies and kinase inhibitors, as well as highlight novel approaches for enhancing immunological responses against tumors. We point out that a fundamental property of the cancer cell, genomic instability, confounds the targeted therapies that aim to induce cell death directly while simultaneously enhancing the potential for immunological attack by creating a large number of neoantigens. We argue for combinatorial strategies with agents that target tumor cells to release these antigens together with innovative therapies that enhance immunological responses by interfering with inhibitory checkpoints.     

Neopepsee: accurate genome-level prediction of neoantigens by harnessing sequence and amino acid immunogenicity information

BackgroundTumor-specific mutations form novel immunogenic peptides called neoantigens. Neoantigens can be used as a biomarker predicting patient response to cancer immunotherapy. Although a predicted binding affinity (IC₅₀) between peptide and major histocompatibility complex class I is currently used for neoantigen prediction, large number of false-positives exist.Materials and methodsWe developed Neopepsee, a machine-learning-based neoantigen prediction program for next-generation sequencing data. With raw RNA-seq data and a list of somatic mutations, Neopepsee automatically extracts mutated peptide sequences and gene expression levels. We tested 14 immunogenicity features to construct a machine-learning classifier and compared with the conventional methods based on IC₅₀ regarding sensitivity and specificity. We tested Neopepsee on independent datasets from melanoma, leukemia, and stomach cancer.ResultsNine of the 14 immunogenicity features that are informative and inter-independent were used to construct the machine-learning classifiers. Neopepsee provides a rich annotation of candidate peptides with 87 immunogenicity-related values, including IC₅₀, expression levels of neopeptides and immune regulatory genes (e.g. PD1, PD-L1), matched epitope sequences, and a three-level (high, medium, and low) call for neoantigen probability. Compared with the conventional methods, the performance was improved in sensitivity and especially two- to threefold in the specificity. Tests with validated datasets and independently proven neoantigens confirmed the improved performance in melanoma and chronic lymphocytic leukemia. Additionally, we found sequence similarity in proteins to known pathogenic epitopes to be a novel feature in classification. Application of Neopepsee to 224 public stomach adenocarcinoma datasets predicted ∼7 neoantigens per patient, the burden of which was correlated with patient prognosis.ConclusionsNeopepsee can detect neoantigen candidates with less false positives and be used to determine the prognosis of the patient. We expect that retrieval of neoantigen sequences with Neopepsee will help advance research on next-generation cancer immunotherapies, predictive biomarkers, and personalized cancer vaccines.