Identification of personalized neoantigen-based vaccines and immune subtype characteristic analysis of glioblastoma based on abnormal alternative splicing

The development of personalized neoantigen-based vaccines in cancer immunotherapy has shown promise. In this study, a large-scale bioinformatics analysis was performed to identify potential GBM-associated neoantigens based on abnormal alternative splicing, and then screen suitable patients for vaccination. Gene expression profiles and clinical information were collected from TCGA. We filtered the percent-spliced-in (PSI) spectrum of alternative splicing events in the dataset to identify abnormal alternative splicing events. MAF package was used to identify and analyse tumour mutation burden (TMB) in cancer samples. Tumour Immune Estimation Resource (TIMER) was used to calculate and visualize the infiltration of antigen presenting cells (APCs). In addition, consistent clustering algorithm utilized to identify immune subtypes of GBM. Five potential tumour neoantigens (LRP1, TCF12, DERL3, WIPI2, and TSHZ3) were identified in GBM by selecting genes both with abnormal alternative splicing (upregulated) and gene frameshift mutations, in which LRP1 was significantly associated with APCs. According to the expressions of five potential tumour neoantigens, 160 patients with GBM were divided into three immune subtypes. Patients in cluster3 exhibited good prognoses. Furthermore, the characteristics, including TMB, abnormal alternative splicing events, immune activity, immune cells proportion, and association with tumour biomarkers, were unique in each immune subtypes. The characteristics of cluster3 illustrated that cluster3 participants were more suitable candidates for vaccination. LRP1 was identified as a potential neoantigen for immunotherapy against GBM, and patients in cluster3 were more suitable for vaccination. Our findings provide important guidance for the development of novel neoantigens and therapeutic targets in patients with GBM.     

Emerging immunotherapies for metastasis

Major advances in cancer immunotherapy have dramatically expanded the potential to manipulate immune cells in cancer patients with metastatic disease to counteract cancer spread and extend patient lifespan. One of the most successful types of immunotherapy is the immune checkpoint inhibitors, such as anti-CTLA-4 and anti-PD-1, that keep anti-tumour T cells active. However, not every patient with metastatic disease benefits from this class of drugs and patients often develop resistance to these therapies over time. Tremendous research effort is now underway to uncover new immunotherapeutic targets that can be used in patients who are refractory to anti-CTLA-4 or anti-PD-1 treatment. Here, we discuss results from experimental model systems demonstrating that modulating the immune response can negatively affect metastasis formation. We focus on molecules that boost anti-tumour immune cells and opportunities to block immunosuppression, as well as cell-based therapies with enhanced tumour recognition properties for solid tumours. We also present a list of challenges in treating metastatic disease with immunotherapy that must be considered in order to move laboratory observations into clinical practice and maximise patient benefit.Subject terms: Tumour immunology, Immunotherapy, Tumour immunology     

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.     

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.     

Integrative tumour mutation burden with CD39 and PD-L1 for the prediction of response to PD-L1 blockade and adjuvant chemotherapy in muscle-invasive bladder cancer patients

Background CD39, a rate-limiting enzyme to convert extracellular ATP (eATP) to adenosine, has been reported to be a key modulator of immune response, but its correlation with therapeutic sensitivity remains obscure. We conducted this study to determine whether the integration of CD39 and traditional biomarkers could improve the prediction of responsiveness to PD-L1 blockade and platinum-based chemotherapy.Methods We retrospectively enrolled a total of 760 patients from IMvigor210 trial, TCGA database and Zhongshan Hospital in this study. We constructed the CPT scoring system based on CD39, PD-L1 and tumour mutation burden (TMB) and validated its efficacy in predicting therapeutic responsiveness in MIBC patients. Kaplan–Meier survival and Cox regression analyses were applied to assess clinical outcomes of patients.Results The CPT scoring system could predict the response to PD-L1 blockade and platinum-based chemotherapy. The CPT score was positively correlated with APOBEC mutational signature and SNV neoantigens enrichment, antigen presentation, and TCR signalling. High CPT score also indicated the inflamed immune phenotype and basal/squamous molecular subtype.Conclusions CD39 expression is closely correlated with the immunogenic contexture of MIBC. Integrating CD39 with PD-L1 and TMB could stratify the sensitivity of patients with MIBC to PD-L1 blockade and platinum-based chemotherapy.Subject terms: Bladder cancer, Cancer immunotherapy, Chemotherapy, Tumour immunology     

The Role of Biomarkers for the Prediction of Response to Checkpoint Immunotherapy and the Rationale for the Use of Checkpoint Immunotherapy in Cervical Cancer

Checkpoint immunotherapy has revolutionised the way that melanoma is treated and has also shown significant effectiveness in lung, bladder, renal, and head and neck cancers. At the present time, trials of checkpoint immunotherapy in cervical cancer are at early phases, but there is very good rationale for pursuing this as a treatment option, especially as cervical cancer is a virally driven cancer and therefore should be recognised by the immune system as being foreign. This review explores the biomarkers for the selection of patients for immunotherapy in other cancers, such as programmed death ligand 1 (PD-L1) expression, tumour infiltrating lymphocytes and total mutational burden, and relates these biomarkers to cervical cancer. A PubMed search was carried out for publications published in English with the terms ‘immunotherapy’ OR ‘cervical cancer’ OR ‘checkpoint blockade’ OR ‘tumour infiltrating lymphocytes’ OR ‘total mutational burden’. Articles that met these criteria and were available on PubMed before 8 October 2018 were included. The results showed that PD-L1 is positive in up to 90% of cervical cancers and that the total mutational burden is moderately high, with 5–6 mutations per megabase. In addition, the tumour microenvironment in cervical cancer has an impact on prognosis, with higher ratios of CD8+ tumour infiltrating lymphocytes to CD4+ T regulatory cells being associated with improved survival. Clinical studies to date have shown the response rate of cervical cancer to checkpoint immunotherapy to be in the region to 10–25%. Cervical cancer exhibits many of the features that have been shown to be correlated with response to checkpoint immunotherapy in other tumour sites. However, response rates to date are in the region of 10–25%. Therefore, combinations of immunotherapeutic agents or checkpoint inhibitors with radiotherapy may be required to maximise the therapeutic benefit of harnessing the host immune system to fight cancer.     

Prognostic significance of the expression levels of T-cell immunoglobulin mucin-3 and its ligand galectin-9 for relapse-free survival in triple-negative breast cancer

T-cell immunoglobulin mucin-3 (TIM-3) expressed at the T-cell surface acts as an immune checkpoint when bound by its ligand galectin-9. Blockade of immunosuppression by the TIM3/galectin-9 signalling pathway may offer novel therapeutic approaches for cancer immunotherapy. Consistent with this, TIM-3 expression is associated with poorer prognosis in several different types of cancer, possibly as a result of suppression of anticancer immunosurveillance. A number of studies have now documented some effectiveness of immune checkpoint blockade even in triple-negative breast cancer (TNBC), which is highly aggressive. However, clinical responses are relatively weak, suggesting that several different pathways may be involved. In this context, the role of the TIM-3/galectin-9 checkpoint in TNBC is not clear. The present study aimed to determine the clinicopathological significance of TIM-3 and galectin-9 expression in this cancer. To this end, 62 patients with TNBC undergoing surgery at Kansai Medical University Hospital (Hirakata, Japan), but not given neoadjuvant chemotherapy, were examined. Tissue microarrays were employed for immunohistochemistry to analyse associations of TIM-3 and galectin-9 expression and their impact on relapse-free survival relative to other poor prognostic risk factors. Galectin-9 expression was detected in 49 of 62 patient samples (79%), and TIM-3 in 30 of them (48.4%). Tumour cell galectin-9 expression was associated with a more favourable prognosis (P=0.027) as was TIM-3 expression on tumour-infiltrating lymphocytes (P=0.007). Multivariate analysis indicated that galectin-9- and TIM-3-double-positivity was significantly associated with a more favourable prognosis compared with galectin-9 and/or TIM-3 negativity (P=0.044). Thus, the TIM-3/galectin-9 signalling pathway may impact anticancer immune reactions in the tumour microenvironment of patients with TNBC. Further investigation will be necessary to determine the molecular mechanisms underlying these relationships.     

Pan-cancer association of HLA gene expression with cancer prognosis and immunotherapy efficacy

Background The function of major histocompatibility complex (MHC) molecules is to bind peptide fragments derived from genomic mutations or pathogens and display them on the cell surface for recognition by cognate T cells to initiate an immune response.Methods In this study, we provide a comprehensive investigation of HLA gene expression in a pan-cancer manner involving 33 cancer types. We utilised gene expression data from several databases and immune checkpoint blockade-treated patient cohorts.Results We show that MHC expression varies strongly among cancer types and is associated with several genomic and immunological features. While immune cell infiltration was generally higher in tumours with higher HLA gene expression, CD4+ T cells showed significantly different correlations among cancer types, separating them into two clusters. Furthermore, we show that increased HLA gene expression is associated with prolonged survival in the majority of cancer types. Lastly, HLA gene expression is associated with patient response to immune checkpoint blockade, which is especially prominent for HLA class II expression in tumour biopsies taken during treatment.Conclusion We show that HLA gene expression is an important feature of tumour biology that has significant impact on patient prognosis.Subject terms: Tumour immunology, MHC     

Cancer immunotherapy: Opportunities and challenges in the rapidly evolving clinical landscape

Cancer immunotherapy is now established as a powerful way to treat cancer. The recent clinical success of immune checkpoint blockade (antagonists of CTLA-4, PD-1 and PD-L1) highlights both the universal power of treating the immune system across tumour types and the unique features of cancer immunotherapy. Immune-related adverse events, atypical clinical response patterns, durable responses, and clear overall survival benefit distinguish cancer immunotherapy from cytotoxic cancer therapy. Combination immunotherapies that transform non-responders to responders are under rapid development. Current challenges facing the field include incorporating immunotherapy into adjuvant and neoadjuvant cancer therapy, refining dose, schedule and duration of treatment and developing novel surrogate endpoints that accurately capture overall survival benefit early in treatment. As the field rapidly evolves, we must prioritise the development of biomarkers to guide the use of immunotherapies in the most appropriate patients. Immunotherapy is already transforming cancer from a death sentence to a chronic disease for some patients. By making smart, evidence-based decisions in developing next generation immunotherapies, cancer should become an imminently treatable, curable and even preventable disease.     

Hypermutated tumours in the era of immunotherapy: The paradigm of personalised medicine

Immune checkpoint inhibitors have demonstrated unprecedented clinical activity in a wide range of cancers. Significant therapeutic responses have recently been observed in patients presenting mismatch repair-deficient (MMRD) tumours. MMRD cancers exhibit a remarkably high rate of mutations, which can result in the formation of neoantigens, hypothesised to enhance the antitumour immune response. In addition to MMRD tumours, cancers mutated in the exonuclease domain of the catalytic subunit of the DNA polymerase epsilon (POLE) also exhibit an ultramutated genome and are thus likely to benefit from immunotherapy. In this review, we provide an overview of recent data on hypermutated tumours, including MMRD and POLE-mutated cancers, with a focus on their distinctive clinicopathological and molecular characteristics as well as their immune environment. We also discuss the emergence of immune therapy to treat these hypermutated cancers, and we comment on the recent Food and Drug Administration approval of an immune checkpoint inhibitor, the programmed cell death 1 antibody (pembrolizumab, Keytruda), for the treatment of patients with metastatic MMRD cancers regardless of the tumour type. This breakthrough represents a turning point in the management of these hypermutated tumours and paves the way for broader strategies in immunoprecision medicine.     

Biomarkers of response to PD-1 pathway blockade

The binding of T cell immune checkpoint proteins programmed death 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) to their ligands allows immune evasion by tumours. The development of therapeutic antibodies, termed checkpoint inhibitors, that bind these molecules or their ligands, has provided a means to release this brake on the host anti-tumour immune response. However, these drugs are costly, are associated with potentially severe side effects, and only benefit a small subset of patients. It is therefore important to identify biomarkers that discriminate between responders and non-responders. This review discusses the determinants for a successful response to antibodies that bind PD-1 or its ligand PD-L1, dividing them into markers found in the tumour biopsy and those in non-tumour samples. It provides an update on the established predictive biomarkers (tumour PD-L1 expression, tumour mismatch repair deficiency and tumour mutational burden) and assesses the evidence for new potential biomarkers.Subject terms: Tumour biomarkers, Cancer immunotherapy, Predictive markers     

免疫检查点抑制剂疗效相关的生物标志物研究进展

肿瘤免疫治疗因其显著的生存获益已成为除手术、化疗、放疗及靶向治疗之外有效的新型肿瘤治疗手段。免疫检查点抑制剂作为肿瘤免疫治疗的方法之一,目前已被批准用于多种晚期肿瘤的治疗。尽管部分肿瘤患者能从中获益,但该抑制剂临床使用过程中的免疫相关不良反应、原发性耐药和继发性耐药等问题限制了其在临床上的广泛应用。免疫检查点抑制剂疗效相关的生物标志物研究有助于患者筛查及个体化治疗,对规范免疫抑制剂单药治疗或联合治疗具有重要意义。     

Biomarkers of Immune Checkpoint Inhibitors in Non–Small Cell Lung Cancer: Beyond PD-L1

Immunotherapy has markedly improved the survival rate of patients with non–small cell lung cancer (NSCLC) and has introduced a new era in lung cancer treatment. Although some patients achieve durable responses to checkpoint blockade, not all experience such benefits, and some suffer from significant immunotoxicities. Thus, it is crucial to identify potential biomarkers suitable for screening the population that may benefit from immunotherapy. Based on the current clinical trials, the aim of the present study was to review the biomarkers for immune checkpoint inhibition that may have the potential to predict the response to immunotherapy in patients with lung cancer. A non-systematic literature review was done. We searched for eligible randomized controlled trials (RCTs) from PubMed, Embase, and the Cochrane Central Register of Controlled Trials from January 2015 to January 2021. The keywords included biomarkers, immunotherapy, immune checkpoint inhibition, programmed death ligand 1 (PD-L1), and non–small cell lung cancer. Additional biomarkers beyond PD-L1 that have been shown to have predictive capacity include tumor mutational burden, microsatellite instability, lung immune prognostic index, gut microbiome, and certain alterations in genes (eg, STK11 deletion, LKB1 kinase mutation, MDM2/4 amplification) that confer immunoresistance. The biomarkers reviewed in this article could help us better select the appropriate immunotherapy treatment for patients with NSCLC.     

Immunonkologische Therapiestrategien

Background

The immune system is principally capable of recognizing and eliminating tumor cells; however, some malignant cells are able to escape immune surveillance by inducing mechanisms of immunoediting and immune evasion. The main idea of cancer immunotherapy is to activate, modulate and amplify host immune responses or to genetically equip the immune repertoire of patients with antitumor specificities and effectors. Nowadays the clinical significance of T-cells in the control of tumor diseases is undisputed. The nature of antigens that allow the immune system to distinguish between “self” and “non-self” has long been unclear. There is considerable evidence that neoantigens play an essential role in the recognition of tumor cells.

Objective

This article presents the three key approaches in cancer immunotherapy in which the focus is on activation of tumor-specific T-cells such as vaccination, checkpoint blockade and adoptive T-cell transfer. Their clinical therapeutic perspective will be discussed.

Methods

A selective literature search was carried out in PubMed.

Results

While the role of tumor vaccination currently remains unresolved, the clinical success of checkpoint blockade and T-cell therapies shows that the therapeutic manipulation of the immune system is a new and already successful cancer immunotherapeutic strategy for some tumor diseases with the potential to significantly improve the overall survival of cancer patients. Some drugs have already gained marketing approval in Europe and USA and others are available for patients in clinical trials.

     

Advances in Combining Radiation and Immunotherapy in Breast Cancer

Breast irradiation has long been utilized in the adjuvant or metastatic setting to eliminate microscopic disease or to palliate existing disease, respectively. However, preclinical data have demonstrated that radiation can also alter the tumor microenvironment and induce antitumor immune responses. As a result, multiple clinical studies have been undertaken and have reported synergy between radiation and immune checkpoint blockade across various cancer types. Given recent clinical successes with immune checkpoint blockade in both early-stage and metastatic breast cancer, there has been substantial interest in combining radiation and immunotherapy to enhance local and systemic immune responses. Herein, we review the preclinical rationale for combining radiotherapy and immunotherapy, the early clinical trials that have adopted this strategy in breast cancer, and the landscape of ongoing relevant clinical trials. Finally, we propose future directions based on promising preclinical studies that integrate radiation, checkpoint blockade, and novel agents for the treatment of breast cancer.     

Immunotherapy of colorectal cancer: Challenges for therapeutic efficacy

A better knowledge of the complex interactions between cancer cells and the immune system has led to novel immunotherapy approaches. Treatment with selective anti-PD1, anti-PD-L1 and/or anti-CTLA-4 monoclonal antibodies (mAbs) has been a revolution in the therapeutic scenario of several cancer types, with the highest clinical efficacy in melanoma and in lung cancer. Colorectal cancer is one of the tumours in which immunotherapy has been shown less effective. Whereas in deficient mismatch repair (MMR) or in highly microsatellite instable (MSI-H) metastatic colorectal cancer there is clear clinical evidence for a therapeutic role of immune checkpoint inhibitors, the vast majority of patients with proficient MMR or with microsatellite stable (MSS) tumours do not benefit from immunotherapy. Defining the molecular mechanisms for immunogenicity in metastatic colorectal cancer is needed in order to develop predictive biomarkers and effective therapeutic combination strategies. A major challenge will be to identify, among the heterogeneous spectrum of this disease, those patients with specific tumour and tumour infiltrating stroma molecular and functional characteristics, that could be effectively treated with immunotherapy. In this review, we discuss the role of immune response in the context of metastatic colorectal cancer. We summarize the available clinical data with the use of anti PD-1/PD-L1 mAbs as single agents or in combination with anti CTLA-4 mAbs in MSI-H patients. Finally, we address the challenges and the potential strategies for rendering the more frequent microsatellite stable (MSS) tumours “immune-competent” and, therefore, amenable for effective immunotherapy interventions.     

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。     

癌症治疗的新兴免疫靶点及相关研究进展

免疫检查点是在机体自身免疫和抗肿瘤作用之间维持平衡的一系列重要因子,通过配体/受体相互作用可识别和启动多条免疫检查点通路,在维持自身免疫耐受和机体免疫稳态中起关键作用,但肿瘤细胞可以利用该途径逃避免疫监视。因此,免疫检查点阻断(immune checkpoint blockade,ICB)通路能够增强抗肿瘤免疫反应,免疫检查点抑制剂应运而生。随着免疫疗法在肿瘤治疗领域取得的重大突破,免疫检查点抑制剂受到越来越多的关注,许多新兴免疫靶点脱颖而出,极具应用前景和临床价值。本文就部分新兴的免疫治疗靶点的特性及相关研究进展进行综述。     

免疫球蛋白超家族受体在肿瘤免疫治疗中的研究进展

近年来免疫检查点阻断在癌症治疗中的应用引起广泛关注。靶向PD-1、PD-L1或CTLA-4的药物在临床试验中仅有部分患者受益。确定新的免疫检查点,探索其作用机制将进一步发展肿瘤免疫疗法。TIGIT、CD226、CD112R和CD96是免疫细胞表达的一组免疫球蛋白超家族受体,与肿瘤细胞表达的Nectin/Necl家族配体（CD155、CD112）相互结合,在肿瘤免疫反应中发挥巨大作用,是新一代的免疫检查点。本文将对CD155、CD112、TIGIT、CD226、CD112R及CD96的分子结构与在肿瘤免疫反应中的作用进行阐述,探讨在癌症免疫治疗中的潜在应用。      

Breast cancer immunobiology driving immunotherapy: vaccines and immune checkpoint blockade

Breast cancer is immunogenic, and infiltrating immune cells in primary breast tumors convey important clinical prognostic and predictive information. Furthermore, the immune system is critically involved in clinical responses to some standard cancer therapies. Early breast cancer vaccine trials have established the safety and bioactivity of breast cancer immunotherapy, with hints of clinical activity. Novel strategies for modulating regulators of immunity, including regulatory T cells, myeloid-derived suppressor cells and immune checkpoint pathways (monoclonal antibodies specific for the cytotoxic T-lymphocyte antigen-4 or programmed death), are now available. In particular, immune checkpoint blockade has enormous therapeutic potential. Integrative breast cancer immunotherapies that strategically combine established breast cancer therapies with breast cancer vaccines, immune checkpoint blockade or both should result in durable clinical responses and increased cures.