Neoantigen cancer vaccines:a new star on the horizon

Immunotherapy represents a promising strategy for cancer treatment that utilizes immune cells or drugs to activate the patient's own immune system and eliminate cancer cells.One of the most exciting advances within this field is the targeting of neoantigens,which are peptides derived from non-synonymous somatic mutations that are found exclusively within cancer cells and absent in normal cells.Although neoantigen-based therapeutic vaccines have not received approval for standard cancer treatment,early clinical trials have yielded encouraging outcomes as standalone monotherapy or when combined with checkpoint inhibitors.Progress made in high-throughput sequencing and bioinformatics have greatly facilitated the precise and efficient identification of neoantigens.Consequently,personalized neoantigen-based vaccines tailored to each patient have been developed that are capable of eliciting a robust and long-lasting immune response which effectively eliminates tumors and prevents recurrences.This review provides a concise overview consolidating the latest clinical advances in neoantigen-based therapeutic vaccines,and also discusses challenges and future perspectives for this innovative approach,particularly emphasizing the potential of neoantigen-based therapeutic vaccines to enhance clinical efficacy against advanced solid tumors.

Colorectal cancer vaccines: Tumor-associated antigens vs neoantigens

Therapeutic options for the treatment of colorectal cancer(CRC) are diverse but still not always satisfying. Recent success of immune checkpoint inhibition treatment for the subgroup of CRC patients suffering from hypermutated tumors suggests a permanent role of immune therapy in the clinical management of CRC. Substantial improvement in treatment outcome could be achieved by development of efficient patient-individual CRC vaccination strategies. This mini-review summarizes the current knowledge on the two general classes of targets: tumor-associated antigens(TAAs) and tumorspecific antigens. TAAs like carcinoembryonic antigen and melanoma associated antigen are present in and shared by a subgroup of patients and a variety of clinical studies examined the efficacy of different TAA-derived peptide vaccines. Combinations of several TAAs as the next step and the development of personalized TAA-based peptide vaccines are discussed. Improvements of peptidebased vaccines achievable by adjuvants and immunestimulatory chemotherapeutics are highlighted. Finally, we sum up clinical studies using tumor-specific antigens-in CRC almost exclusively neoantigens-which revealed promising results; particularly no severe adverse events were reported so far. Critical progress for clinical outcomes can be expected by individualizing neoantigen-based peptide vaccines and combining them with immunestimulatory chemotherapeutics and immune checkpoint inhibitors. In light of these data and latest developments, truly personalized neoantigen-based peptide vaccines can be expected to fulfill modern precision medicine's requirements and will manifest as treatment pillar for routine clinical management of CRC.

Profiling of hepatocellular carcinoma neoantigens reveals immune microenvironment and clonal evolution related patterns

Objective: Neoantigens derived from tumor-specific genomic alterations have demonstrated great potential for immunotherapeutic interventions in cancers. However, the comprehensive profile of hepatocellular carcinoma(HCC) neoantigens and their complex interplay with immune microenvironment and tumor evolution have not been fully addressed.Methods: Here we integrated whole exome sequencing data, transcriptome sequencing data and clinical information of 72 primary HCC patients to characterize the HCC neoantigen profile, and systematically explored its interactions with tumor clonal evolution, driver mutations and immune microenvironments.Results: We observed that higher somatic mutation/neoantigen load was associated with better clinical outcomes and HCC patients could be further divided into two subgroups with distinct prognosis based on their neoantigen expression patterns. HCC subgroup with neoantigen expression probability high(NEP-H) showed more aggressive pathologic features including increased incidence of tumor thrombus(P=0.038), higher recurrence rate(P=0.029),more inclined to lack tumor capsule(P=0.026) and with more microsatellite instability sites(P=0.006). In addition,NEP-H subgroup was also characterized by higher chance to be involved in tumor clonal evolution [odds ratio(OR)=46.7, P<0.001]. Gene set enrichment analysis revealed that upregulation of MYC and its targets could suppress immune responses, leading to elevated neoantigen expression proportion in tumor cells. Furthermore, we discovered an immune escape mechanism that tumors could become more inconspicuous by evolving subclones with less immunogenicity. We observed that smaller clonal mutation clusters with higher immunogenicity in tumor were more likely to involve in clonal evolution. Based on identified neoantigen profiles, we also discovered series of neoantigenic hotspot genes, which could serve as potential actionable targets in future.Conclusions: Our results revealed the landscape of HCC neoantigens and discovered two clinically relevant subgroups with distinct neoantigen expression patterns, suggesting the neoantigen expression should be fully considered in future immunotherapeutic interventions.

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.

Prediction of neoantigens and their application in cancer treatment

Tumor antigens can be divided into tumor-associated antigens and tumor-specific antigens according to their specificity. Tumorassociated antigens are not unique to tumor cells, and can also be synthesized in small amounts by normal cells. Tumor-specific antigens, also called neoantigens, are formed by peptides that are entirely absent from the normal human genome [1]. Neoantigens are

NeoHunter:Flexible software for systematically detecting neoantigens from sequencing data

Complicated molecular alterations in tumors generate various mutant peptides.Some of these mutant peptides can be presented to the cell surface and then elicit immune responses,and such mutant peptides are called neoantigens.Accurate detection of neoantigens could help to design personalized cancer vaccines.Although some computational frameworks for neoantigen detection have been proposed,most of them can only detect SNV-and indel-derived neoantigens.In addition,current frameworks adopt oversimplified neoantigen prioritization strategies.These factors hinder the comprehensive and effective detection of neoantigens.We developed NeoHunter,flexible software to systematically detect and prioritize neoantigens from sequencing data in different formats.NeoHunter can detect not only SNV-and indel-derived neoantigens but also gene fusion-and aberrant splicing-derived neoantigens.NeoHunter supports both direct and indirect immunogenicity evaluation strategies to prioritize candidate neoantigens.These strategies utilize binding characteristics,existing biological big data,and T-cell receptor specificity to ensure accurate detection and prioritization.We applied NeoHunter to the TESLA dataset,cohorts of melanoma and non-small cell lung cancer patients.NeoHunter achieved high performance across the TESLA cancer patients and detected 79%(27 out of 34)of validated neoantigens in total.SNV-and indel-derived neoantigens accounted for 90%of the top 100 candidate neoantigens while neoantigens from aberrant splicing accounted for 9%.Gene fusion-derived neoantigens were detected in one patient.NeoHunter is a powerful tool to‘catch all’neoantigens and is available for free academic use on Github(XuegongLab/NeoHunter).

TSNAdb v2.0:The Updated Version of Tumor-specific Neoantigen Database

In recent years,neoantigens have been recognized as ideal targets for tumor immunotherapy.With the development of neoantigen-based tumor immunotherapy,comprehensive neoantigen databases are urgently needed to meet the growing demand for clinical studies.We have built the tumor-specific neoantigen database(TSNAdb)previously,which has attracted much attention.In this study,we provide TSNAdb v2.0,an updated version of the TSNAdb.TSNAdb v2.0 offers several new features,including(1)adopting more stringent criteria for neoantigen identification,(2)providing predicted neoantigens derived from three types of somatic mutations,and(3)collecting experimentally validated neoantigens and dividing them according to the experimental level.

Ionizable polymeric nanocarriers for the codelivery of bi-adjuvant and neoantigens in combination tumor immunotherapy

Ionizable lipid nanocarriers have made historical contribution to COVID-19 mRNA vaccines.Here,we report ionizable polymeric nanoparticles that co-deliver bi-adjuvant and neoantigen peptides for cancer immunotherapy in combination with immune checkpoint blockade(ICB).Current cancer ICB benefits only a small subset of patients,largely due to a lack of pre-existing target cells and checkpoint targets for ICB,tumor antigenic heterogeneity,and tumor immunosuppression.Therapeutic vaccines hold the potential to enhance ICB therapeutic efficacy by expanding antitumor cell repertoires,upregulating immune checkpoint levels and hence sensitizing ICB,and reducing tumor immunosuppression.Chemically defined peptide vaccines are attractive,but their current therapeutic efficacy has been limited due to 1)poor vaccine delivery to immunomodulatory lymph nodes(LNs)and antigen(Ag)-presenting cells(APCs),2)poor immunostimulant adjuvant efficacy with restricted target cell subsets in humans,3)limited adjuvant/Ag codelivery to enhance Ag immunogenicity,and 4)limited ability to overcome tumor antigenic heterogeneity.Here,we developed nanovaccines(NVs)using pH-responsive polymeric micellular nanoparticles(NPs)for the codelivery of bi-adjuvant[Toll-like receptor(TLR)7/8 agonist R848 and TLR9 agonist CpG]and peptide neoantigens(neoAgs)to draining LNs for efficient Ag presentation in a broad range of APC subsets.These NVs potentiated the immunogenicity of peptide Ags and elicits robust antitumor T cell responses with memory,and remodeled the tumor immune milium with reduced tumor immunosuppression.As a result,NVs significantly enhanced ICB therapeutic efficacy for murine colorectal tumors and orthotopic glioblastoma multiforme(GBM).These results suggest marked potential of bi-adjuvant/neoAg-codelivering NVs for combination cancer immunotherapy.

黑色素瘤个体化治疗策略:基于新抗原的特异性免疫治疗

免疫检查点抑制剂显著改善黑色素瘤患者预后,但原发及继发性耐药使治疗进入瓶颈期。T细胞受体与肿瘤抗原的结合是免疫治疗发挥作用的关键。肿瘤新抗原(neoantigen)由肿瘤特异性蛋白编码突变产生,在肿瘤细胞中特异表达,在正常组织不表达,不受中枢免疫耐受影响,是免疫治疗的理想靶点。靶向肿瘤新抗原的疫苗、过继性细胞回输及抗体药物等能有效加强和扩大肿瘤特异性免疫反应,促进T细胞识别并清除肿瘤,突破当前治疗瓶颈。本文就黑色素瘤新抗原的个性化治疗现状、最新进展、临床困境及未来发展方向进行讨论分析。

合成生物学在肿瘤疫苗设计中的应用进展

根据中心法则和细胞免疫学原则,利用合成生物学设计和生产新型肿瘤疫苗代表了癌症免疫治疗中的一个重要途径。本文概述了利用合成生物学针对两个主要方面(抗原选择和疫苗设计)的创新治疗性肿瘤疫苗的最新研究进展。针对肿瘤相关或特定抗原,开发更精确和有效的肿瘤疫苗引起了广泛关注。传统方法在抗原选择中主要针对肿瘤中的特定基因,而以高通量测序及质谱为基础筛选新抗原的方法明显改善了疫苗的靶向性及免疫原性。在疫苗类别方面,与传统多肽疫苗相比,通过对DNA、mRNA、病毒/细菌、细胞的工程化修饰而成的新型疫苗显著扩大了肿瘤疫苗的范围,从而大幅增强了不同肿瘤疫苗的免疫效果。合成生物学的快速发展将加速对肿瘤疫苗的实验研究进度,最终导致临床治疗效果的持续增强。

新抗原脉冲树突状细胞疫苗在肿瘤免疫治疗中的作用

新抗原脉冲树突状细胞疫苗(Neo-DCVac)是一种新型肿瘤免疫治疗手段。新抗原是指肿瘤细胞突变产生的具有较强免疫原性和肿瘤特异性的肽段。Neo-DCVac是基于新抗原被树突状细胞摄取、加工后递呈并激活T细胞引发机体免疫反应,从而发挥抗肿瘤作用。在高通量测序基础上发展而来的个体化Neo-DCVac有望成为肿瘤精准免疫治疗的新方向。本文从个体化Neo-DCVac构建、在实体瘤中联合治疗的临床应用、适宜接种人群和目前存在的局限性等方面进行综述,旨在为肿瘤免疫治疗的相关研究提供参考。

Wilm′s tumor gene1肽疫苗Galinpepimut-S在肿瘤免疫治疗中的应用

目的为Wilm′s tumor gene1(WT1)肽疫苗Galinpepimut-S(GPS)用于肿瘤免疫治疗的后续研究提供参考。方法采用计算机检索中国知网、PubMed等数据库自建库起至2022年12月的肿瘤免疫治疗相关文献,总结GPS在肿瘤免疫治疗中的应用现状。结果GPS能激发自身免疫系统,对WT1抗原产生强烈免疫反应而发挥抗肿瘤作用,在卵巢癌、恶性胸膜间皮瘤、急性髓系白血病、多发性骨髓瘤的治疗中均显示出较好的疗效。结论以GPS为代表的肿瘤疫苗是未来肿瘤治疗的重要方向,需进一步进行临床研究,以获取更多数据。

肿瘤新抗原疫苗的设计与优化策略

随着免疫检查点抑制剂和嵌合抗原受体T细胞疗法在不同适应证中的研究和临床应用,免疫治疗已经彻底改变了多种肿瘤的治疗方式。肿瘤新抗原疫苗作为一种前景广阔的免疫治疗方法,旨在激发针对新抗原的特异性T细胞反应。新抗原具有高度特异性,能够诱导和扩展肿瘤特异性T细胞库,即表位扩展。初步临床研究表明,通过快速、经济、高效的合成生物学技术,新抗原肿瘤疫苗已经展现出强大的肿瘤特异性免疫原性和抗肿瘤活性的初步证据。本文详细探讨了肿瘤新抗原的来源、发现与鉴定,以及新抗原疫苗的分类和免疫接种方案。还总结了肿瘤新抗原疫苗的优化策略,包括对预测算法、疫苗结构、免疫原性、给药方式和递送系统等方面的优化,以及联合佐剂、放化疗、免疫检查点抑制剂等方式,为个性化免疫疗法的发展提供了新的思路。

mRNA肿瘤疫苗:研究进展及临床应用前景

免疫疗法为肿瘤治疗提供了有效的辅助作用,其中信使RNA(messenger RNA,mRNA)肿瘤疫苗有着较好的肿瘤免疫激活作用,为肿瘤辅助治疗提供了一个潜在的应用前景。mRNA疫苗能够激活或者增强人体免疫系统特异性识别抗原的能力,从而实现抗肿瘤作用。相比较于其他疫苗平台,mRNA肿瘤疫苗具有安全、不被整合、负载多种抗原等特点。肿瘤的不同突变类型导致了肿瘤治疗存在一定的个体差异性,肿瘤抗原的选择就显得尤为重要。同时,mRNA修饰可以增强mRNA的稳定性及翻译效率。这些因素都影响着mRNA疫苗的抗肿瘤效应。目前多种个体化mRNA肿瘤疫苗在临床试验中表现出较好的安全性及免疫原性。因此,通过本综述能更好的了解mRNA肿瘤疫苗的作用以及开发个性化肿瘤疫苗的临床价值,并且联合现有的治疗方式能为肿瘤辅助治疗提供更为有效的治疗方案。

TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis

Tumor-specific neoantigens have attracted much attention since they can be used as biomarkers to predict therapeutic effects of immune checkpoint blockade therapy and as potential targets for cancer immunotherapy. In this study, we developed a comprehensive tumor-specific neoantigen database （TSNAdb v1.0）, based on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte antigen （HLA） allele information for 16 tumor types with 7748 tumor samples from The Cancer Genome Atlas （TCGA） and The Cancer Immunome Atlas （TCIA）. We predicted binding affinities between mutant/wild-type peptides and HLA class I molecules by NetMHCpan v2.8/v4.0, and presented detailed information of 3,707,562/1,146,961 potential neoantigens generated by somatic mutations of all tumor samples. Moreover, we employed recurrent mutations in combination with highly frequent HLA alleles to predict potential shared neoantigens across tumor patients,which would facilitate the discovery of putative targets for neoantigen-based cancer immunotherapy.TSNAdb is freely available at http：//biopharm.zju.edu.cn/tsnadb.

Neoantigens in precision cancer immunotherapy:from identification to clinical applications

Immunotherapies targeting cancer neoantigens are safe,effective,and precise.Neoantigens can be identified mainly by genomic techniques such as next-generation sequencing and high-throughput single-cell sequencing;proteomic techniques such as mass spectrometry;and bioinformatics tools based on high-throughput sequencing data,mass spectrometry data,and biological databases.Neoantigen-related therapies are widely used in clinical practice and include neoantigen vaccines,neoantigen-specific CD8+and CD4+T cells,and neoantigen-pulsed dendritic cells.In addition,neoantigens can be used as biomarkers to assess immunotherapy response,resistance,and prognosis.Therapies based on neoantigens are an important and promising branch of cancer immunotherapy.Unremitting efforts are needed to unravel the comprehensive role of neoantigens in anti-tumor immunity and to extend their clinical application.This review aimed to summarize the progress in neoantigen research and to discuss its opportunities and challenges in precision cancer immunotherapy.

Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines

Molecular-assisted precision oncology gained tremendous ground with high-throughput next-generation sequencing(NGS),supported by robust bioinformatics.The quest for genomicsbased cancer medicine set the foundations for improved patient stratification,while unveiling a wide array of neoantigens for immunotherapy.Upfront pre-clinical and clinical studies have successfully used tumor-specific peptides in vaccines with minimal off-target effects.However,the low mutational burden presented by many lesions challenges the generalization of these solutions,requiring the diversification of neoantigen sources.Oncoproteogenomics utilizing customized databases for protein annotation by mass spectrometry(MS)is a powerful tool toward this end.Expanding the concept toward exploring proteoforms originated from post-translational modifications(PTMs)will be decisive to improve molecular subtyping and provide potentially targetable functional nodes with increased cancer specificity.Walking through the path of systems biology,we highlight that alterations in protein glycosylation at the cell surface not only have functional impact on cancer progression and dissemination but also originate unique molecular fingerprints for targeted therapeutics.Moreover,we discuss the outstanding challenges required to accommodate glycoproteomics in oncoproteogenomics platforms.We envisage that such rationale may flag a rather neglected research field,generating novel paradigms for precision oncology and immunotherapy.

Neoantigen vaccine and neoantigen-specific cell adoptive transfer therapy in solid tumors:Challenges and future directions

The phenomenon of tumor hierarchy and genetic instability can be explained by the“two-hits theory”and results in the occurrence of many somatic mutations.The expression of nonsynonymous mutations results in the production of mutant proteins from tumor cells,namely tumor-specific antigens called neoantigens.Because neoantigens do not exist in healthy cells,they have the potential to stimulate antitumor immune responses by CD4+and CD8+T-cell activation without jeopardizing normal tissues.Immunotherapy has reshaped the cancer treatment paradigm in recent decades with the introduction of immune-checkpoint blockade therapy and transgenic Tcell receptor/chimeric antigen receptor T cells.However,these strategies performed poorly in solid tumors because of the obstacles of the immunosuppressive microenvironment caused by regulatory T cells and other suppressor cells.Therefore,other immunotherapeutic strategies are under development,such as personalized vaccines,to trigger de novo T-cell responses against neoantigens and lead to the amplification of tumorspecific T-cell subclones.Neoantigen epitope prediction algorithms have enabled the detection of neoantigens and the creation of tailored neoantigen vaccines as a result of the fast development of next-generation sequencing and cancer bioinformatics.Here we provide an overview of the current neoantigen cancer vaccines and adoptive T-cell transfer therapy with neoantigen-specific lymphocytes.We also discuss the challenges in developing neoantigentargeted immunotherapeutic strategies for cancer.

Combination immunotherapy of glioblastoma with dendritic cell cancer vaccines,anti-PD-1 and poly I:C

Glioblastoma(GBM)is a lethal cancer with limited therapeutic options.Dendritic cell(DC)-based cancer vaccines provide a promising approach for GBM treatment.Clinical studies suggest that other immunotherapeutic agents may be combined with DC vaccines to further enhance antitumor activity.Here,we report a GBM case with combination immunotherapy consisting of DC vaccines,anti-programmed death-1(anti-PD-1)and poly I:C as well as the chemotherapeutic agent cyclophosphamide that was integrated with standard chemoradiation therapy,and the patient remained disease-free for 69 months.The patient received DC vaccines loaded with multiple forms of tumor antigens,including mRNA-tumor associated antigens(TAA),mRNA-neoantigens,and hypochlorous acid(HOCl)-oxidized tumor lysates.Furthermore,mRNA-TAAs were modified with a novel TriVac technology that fuses TAAs with a destabilization domain and inserts TAAs into full-length lysosomal associated membrane protein-1 to enhance major histocompatibility complex(MHC)class I and II antigen presentation.The treatment consisted of 42 DC cancer vaccine infusions,26 anti-PD-1 antibody nivolumab administrations and 126 poly I:C injections for DC infusions.The patient also received 28 doses of cyclophosphamide for depletion of regulatory T cells.No immunotherapy-related adverse events were observed during the treatment.Robust antitumor CD4t and CD8t T-cell responses were detected.The patient remains free of disease progression.This is the first case report on the combination of the above three agents to treat glioblastoma patients.Our results suggest that integrated combination immunotherapy is safe and feasible for long-term treatment in this patient.A large-scale trial to validate these findings is warranted.

治疗性肿瘤疫苗:过去、现在和未来

肿瘤是机体在各种致瘤因素的作用下,局部细胞在基因水平上对其生长的调控失去控制,导致细胞异常增生而形成的新生物。根据肿瘤生物学特性及其对机体危害程度的不同,可将其分为良性和恶性肿瘤两大类。在中国,恶性肿瘤是导致患者死亡的主要原因之一,其发病率和死亡率不断攀升,成为非常严重的公共健康问题。肿瘤疫苗是一种利用肿瘤特异性抗原或肿瘤相关抗原激活机体特异性免疫应答,以杀伤肿瘤细胞的免疫干预策略,是肿瘤免疫治疗研究的热点之一。在过去的几十年里,随着基因技术的不断发展,肿瘤疫苗的研发取得了极大的进步。肿瘤疫苗在实体瘤的临床前研究及其相关试验中均显示出巨大的潜力,有望进一步提高患者的总生存期。根据作用目的,肿瘤疫苗可分为预防性肿瘤疫苗和治疗性肿瘤疫苗;根据作用机制,肿瘤疫苗又可分为细胞疫苗、蛋白质/合成肽疫苗、核酸疫苗等。目前,免疫检查点抑制剂、过继性细胞治疗和基于纳米材料的免疫疗法均在肿瘤治疗中显示出较好的疗效,肿瘤疫苗同其它免疫疗法的联合应用有可能成为肿瘤治疗领域的未来方向。然而,肿瘤疫苗的发展历经重重困难,但也积累了宝贵的临床研发经验。本文主要就不同类型治疗性肿瘤疫苗的起源、类型、作用机制及其优势与局限性展开论述,以期为今后肿瘤疫苗的研究工作提供帮助。