Forward Vaccinology: CTL Targeting Based upon Physical Detection of HLA-Bound Peptides

ALK peptide vaccination restores the immunogenicity of ALK-rearranged non-small cell lung cancer

Anaplastic lymphoma kinase (ALK)-rearranged non-small cell lung cancer (NSCLC) is treated with ALK tyrosine kinase inhibitors (TKIs), but the lack of activity of immune checkpoint inhibitors (ICIs) is poorly understood. Here, we identified immunogenic ALK peptides to show that ICIs induced rejection of ALK+ tumors in the flank but not in the lung. A single-peptide vaccination restored priming of ALK-specific CD8+ T cells, eradicated lung tumors in combination with ALK TKIs and prevented metastatic dissemination of tumors to the brain. The poor response of ALK+ NSCLC to ICIs was due to ineffective CD8+ T cell priming against ALK antigens and is circumvented through specific vaccination. Finally, we identified human ALK peptides displayed by HLA-A*02:01 and HLA-B*07:02 molecules. These peptides were immunogenic in HLA-transgenic mice and were recognized by CD8+ T cells from individuals with NSCLC, paving the way for the development of a clinical vaccine to treat ALK+ NSCLC.

CTLs: Killers of intracellular bacteria

Many microbial pathogens have evolved a range of capabilities to evade host immune defense mechanisms and to survive and multiply in host cells. The presence of host intracellular bacteria makes it difficult for specific antibodies to function. After the intracellular bacteria escape the attack of the innate immune system, such as phagocytes, they survive in cells, and then adaptive immunity comes into play. Cytotoxic T lymphocytes (CTLs) play an important role in eliminating intracellular bacteria. The regulation of key transcription factors could promote CD4+/CD8+ T cells to acquire cytolytic ability. The TCR-CD3 complex transduces activation signals generated by TCR recognition of antigen and promotes CTLs to generate multiple pathways to kill intracellular bacteria. In this review, the mechanism of CD4/CD8 CTLs differentiation and how CD4/CD8 CTLs kill intracellular bacteria are introduced. In addition, their application and prospects in the treatment of bacterial infections are discussed.

TANTIGEN: a comprehensive database of tumor T cell antigens

Tumor T cell antigens are both diagnostically and therapeutically valuable molecules. A large number of new peptides are examined as potential tumor epitopes each year, yet there is no infrastructure for storing and accessing the results of these experiments. We have retroactively cataloged more than 1000 tumor peptides from 368 different proteins, and implemented a web-accessible infrastructure for storing and accessing these experimental results. All peptides in TANTIGEN are labeled as one of the four categories: (1) peptides measured in vitro to bind the HLA, but not reported to elicit either in vivo or in vitro T cell response, (2) peptides found to bind the HLA and to elicit an in vitro T cell response, (3) peptides shown to elicit in vivo tumor rejection, and (4) peptides processed and naturally presented as defined by physical detection. In addition to T cell response, we also annotate peptides that are naturally processed HLA binders, e.g., peptides eluted from HLA in mass spectrometry studies. TANTIGEN provides a rich data resource for tumor-associated epitope and neoepitope discovery studies and is freely available at http://cvc.dfci.harvard.edu/tantigen/ or http://projects.met-hilab.org/tadb (mirror).

Antigenic variability: Obstacles on the road to vaccines against traditionally difficult targets

Despite the impressive impact of vaccines on public health, the success of vaccines targeting many important pathogens and cancers has to date been limited. The burden of infectious diseases today is mainly caused by antigenically variable pathogens (AVPs), which escape immune responses induced by prior infection or vaccination through changes in molecular structures recognized by antibodies or T cells. Extensive genetic and antigenic variability is the major obstacle for the development of new or improved vaccines against "difficult" targets. Alternative, qualitatively new approaches leading to the generation of disease- and patient-specific vaccine immunogens that incorporate complex permanently changing epitope landscapes of intended targets accompanied by appropriate immunomodulators are urgently needed. In this review, we highlight some of the most critical common issues related to the development of vaccines against many pathogens and cancers that escape protective immune responses owing to antigenic variation, and discuss recent efforts to overcome the obstacles by applying alternative approaches for the rational design of new types of immunogens.

αβ TCR-mediated recognition: relevance to tumor-antigen discovery and cancer immunotherapy

αβ T lymphocytes sense perturbations in host cellular body components induced by infectious pathogens, oncogenic transformation, or chemical or physical damage. Millions to billions of these lymphocytes are generated through T-lineage development in the thymus, each endowed with a clonally restricted surface T-cell receptor (TCR). An individual TCR has the capacity to recognize a distinct "foreign" peptide among the myriad of antigens that the mammalian host must be capable of detecting. TCRs explicitly distinguish foreign from self-peptides bound to major histocompatibility complex (MHC) molecules. This is a daunting challenge, given that the MHC-linked peptidome consists of thousands of distinct peptides with a relevant nonself target antigen often embedded at low number, among orders of magnitude higher frequency self-peptides. In this Masters of Immunology article, I review how TCR structure and attendant mechanobiology involving nonlinear responses affect sensitivity as well as specificity to meet this requirement. Assessment of human tumor-cell display using state-of-the-art mass spectrometry physical detection methods that quantify epitope copy number can help to provide information about requisite T-cell functional avidity affording protection and/or therapeutic immunity. Future rational CD8 cytotoxic T-cell-based vaccines may follow, targeting virally induced cancers, other nonviral immunogenic tumors, and potentially even nonimmunogenic tumors whose peptide display can be purposely altered by MHC-binding drugs to stimulate immune attack.

Role of Ets Proteins in Development, Differentiation, and Function of T-Cell Subsets

Through positive selection, double-positive cells in the thymus differentiate into CD4(+) or CD8(+) T single-positive cells that subsequently develop into different types of effective T cells, such as T-helper and cytotoxic T lymphocyte cells, that play distinctive roles in the immune system. Development, differentiation, and function of thymocytes and CD4(+) and CD8(+) T cells are controlled by a multitude of secreted and intracellular factors, ranging from cytokine signaling modules to transcription factors and epigenetic modifiers. Members of the E26 transformation specific (Ets) family of transcription factors, in particular, are potent regulators of these CD4(+) or CD8(+) T-cell processes. In this review, we summarize and discuss the functions and underlying mechanisms of the Ets family members that have been characterized as involved in these processes. Ongoing research of these factors is expected to identify practical applications for the Ets family members as novel therapeutic targets for inflammation-related diseases.

Characterization of Plasmodium falciparum Proteome at Asexual Blood Stages for Screening of Effective Vaccine Candidates: An Immunoinformatics Approach

Malaria is a complex parasitic disease that is currently causing great concerns globally owing to the resistance to antimalarial drugs and lack of an effective vaccine. The present study involves the characterization of extracellular secretory proteins as vaccine candidates derived from proteome analysis of Plasmodium falciparum at asexual blood stages of malaria. Among the screened 32 proteins, 31 were predicted as antigens by the VaxiJen program, and 26 proteins had less than two transmembrane spanning regions predicted using the THMMM program. Moreover, 10 and 5 proteins were predicted to contain secretory signals by SignalP and TargetP, respectively. T-cell epitope prediction using MULTIPRED2 and NetCTL programs revealed that most of the predicted antigens are immunogenic and contain more than 10% supertype and 5% promiscuous epitopes of HLA-A, -B, or -DR. We anticipate that T-cell immune responses against asexual blood stages of Plasmodium are dispersed on a relatively large number of parasite antigens. This is the first report, to the best of our knowledge, offering new insights, at the proteome level, for the putative screening of effective vaccine candidates against the malaria pathogen. The findings also suggest new ways forward for the modern omics-guided vaccine target discovery using reverse vaccinology.

Cancer prevention: state of the art and future prospects

Cancer imposes a heavy societal burden worldwide, in terms of both epidemiology and costs. The introduction of more sophisticated imaging and diagnostic techniques and advanced drugs that specifically target tumor cells is leading to increasingly expensive treatments, which may be affordable only for few patients. Prevention, and particularly primary prevention, is an effective way of addressing the challenging issue of cancer, since between a third and a half of cancers could be prevented on the basis of our current knowledge of risk factors. Moreover, prevention is cost-effective, its effects are not limited to high-risk subjects but extend to the entire population, and it is not dependent on socioeconomic status. Regulatory measures can have a broad impact, even on future generations; by empowering and educating subjects, promoting healthy behaviours and teaching self-care, they can trigger a virtuous cycle. In recent decades, oncology has shifted from being merely reactive to being proactive; this shift has led to the development of so-called "P4 medicine", where the 4 Ps stand for "preventive", "predictive", "personalized" and "participatory". Prevention programs are an important part of the effort to control cancer, as they are able to reduce both the incidence of cancer and mortality. For instance, screening for colorectal, breast and cervical cancer is reducing the burden of these common tumors. Anti-cancer vaccines, both prophylactic and therapeutic, constitute another important preventive tool. Although progress has been made in these areas, much remains to be done. With regard to screening programs, coverage could be increased by introducing new, more acceptable, less invasive tests, stratifying screening through correlation with anamnestic, clinical, radiological and genomic data (so-called "populationbased personalized cancer screening"), and exploiting new information and communication technologies, such as smartphone applications or personalized text messages (so-called "screening 2.0"). Advocacy and recommendations by physicians can also play a role, in that eligible subjects need to be able to discuss their doubts and their perceived psycho-social barriers. However, new screening initiatives should be implemented only after a careful health technology assessment has been performed within the framework of evidence-based medicine, organized screening programs have been strengthened and opportunistic or spontaneous programs have been limited.