Prediction of cancer neoepitopes needs new rules

Aggregation-prone peptides from within a non-self-protein homoaggregate are preferred for MHC association: Historical overview

New technologies assist re-evaluation of hypotheses on generation of immune cell repertoires and distinctions of self from non-self. Findings include positive correlations between peptide propensities to aggregate and their binding to major histocompatibility complex (MHC) proteins. This recalls the hypothesis that foreign proteins may homoaggregate in host cytosols prior to releasing their peptides (p) to form pMHC complexes. Clues to this included aggregation-related phenomena associated with infections (rouleaux formation, pyrexia, certain brain diseases). By virtue of 'promiscuous' gene expression by thymic presenting cells - perhaps adapted from earlier evolving gonadal mechanisms - developing T cells monitor surface pMHC clusterings. This evaluates intracellular concentrations of the corresponding proteins, and hence, following Burnet's two signal principle, degrees of self-reactivity. After positive selection in the thymic cortex for reactivity with 'near-self', high-level pMHC clustering suffices in the medulla for negatively selection. Following Burnet's principle, in the periphery low-level clustering suffices for T cell stimulation and high-level clustering again provokes negative selection (immunological tolerance). For evolving intracellular pathogens, fine-tuned polymorphisms of their host species have limited to 'near-self' some mimicking adaptations. It is proposed that while entire pathogen proteins may have evolved to minimize their aggregability, the greater aggregability of their peptides remains partially hidden within. Two-step proofreading mechanisms in prospective hosts select proteins containing aggregable peptide for the generation of pMHC clusters at the surface of presenting cells. Through mutations, some proteins of pathogens and cancer cells tend to converge towards the host 'near-self' that its T cells have auditioned to address.

Interferon-α promotes neo-antigen formation and preferential HLA-B-restricted antigen presentation in pancreatic β-cells

Interferon (IFN)-α is the earliest cytokine signature observed in individuals at risk for type 1 diabetes (T1D), but its effect on the repertoire of HLA Class I (HLA-I)-bound peptides presented by pancreatic β-cells is unknown. Using immunopeptidomics, we characterized the peptide/HLA-I presentation in in-vitro resting and IFN-α-exposed β-cells. IFN-α increased HLA-I expression and peptide presentation, including neo-sequences derived from alternative mRNA splicing, post-translational modifications - notably glutathionylation - and protein cis-splicing. This antigenic landscape relied on processing by both the constitutive and immune proteasome. The resting β-cell immunopeptidome was dominated by HLA-A-restricted ligands. However, IFN-α only marginally upregulated HLA-A and largely favored HLA-B, translating into a major increase in HLA-B-restricted peptides and into an increased activation of HLA-B-restricted vs. HLA-A-restricted CD8+ T-cells. A preferential HLA-B hyper-expression was also observed in the islets of T1D vs. non-diabetic donors, and we identified islet-infiltrating CD8+ T-cells from T1D donors reactive to HLA-B-restricted granule peptides. Thus, the inflammatory milieu of insulitis may skew the autoimmune response toward epitopes presented by HLA-B, hence recruiting a distinct T-cell repertoire that may be relevant to T1D pathogenesis.

Application of microneedles combined with dendritic cell-targeted nanovaccine delivery system in percutaneous immunotherapy for triple-negative breast cancer

This work aims at developing a strategy to activate the antigen-presenting cells to enhance the effect of immunotherapy in triple-negative breast cancer (TNBC) through the dissolving microneedle patch (DMNP). In present study, mannosylated chitosan (MCS) nanoparticles (NPs) were designed to target dendritic cells (DCs), and the immunotherapy effect was enhanced by the adjuvant Bacillus Calmette-Guerin polysaccharide (BCG-PSN), achieving the purpose of transdermal immunotherapy for TNBC. Vaccination studies with mice demonstrated that MCS NPs effectively induce DCs maturation in the tumor-draining lymph nodes to stimulate strong immune responses in TNBC. Overall, chitosan-based DMNPs with complex adjuvant constituted a new potent transdermal vaccine delivery platform capable of exploiting more DCs in the skin for effective immunization.

β2-microglobulin and colorectal cancer among inpatients: a case-control study

Β2-microglobulin (β2-M) is associated with various malignancies. However, the relationship between β2-M and colorectal cancer (CRC) remains unclear. We explored the association between β2-M and CRC among inpatients who underwent colonoscopy and explored factors that may modify the association. All consecutive inpatients who underwent colonoscopy were enrolled in a tertiary hospital between April 2015 and June 2022. Inpatients with initial CRC or normal colonoscopies were considered eligible as cases or controls, respectively. Baseline characteristics and laboratory indicators of the participants were collected from electronic medical records. Logistic regression analysis, smooth curve fitting, sensitivity analysis, and subgroup analysis were conducted in the present study. After adjusting for baseline clinical characteristics and laboratory parameters, β2-M was positively associated with CRC (odds ratio [OR] 1.32; 95% confidence interval [CI] 1.11-1.58) among inpatients. When the β2-M level was assigned as tertiles, participants in the highest tertile presented with a higher risk of CRC (OR 2.33; 95% CI 1.57-3.48). A positive linear association was observed between β2-M and CRC with smooth curve fitting. In particular, it may be of great importance to monitor β2-M levels for predicting CRC patients.

Unraveling tumor specific neoantigen immunogenicity prediction: a comprehensive analysis

Introduction

Identification of tumor specific neoantigen (TSN) immunogenicity is crucial to develop peptide/mRNA based anti-tumoral vaccines and/or adoptive T-cell immunotherapies; thus, accurate in-silico classification/prioritization proves critical for cost-effective clinical applications. Several methods were proposed as TSNs immunogenicity predictors; however, comprehensive performance comparison is still lacking due to the absence of well documented and adequate TSN databases.

Methods

Here, by developing a new curated database having 199 TSNs with experimentally-validated MHC-I presentation and positive/negative immune response (ITSNdb), sixteen metrics were evaluated as immunogenicity predictors. In addition, by using a dataset emulating patient derived TSNs and immunotherapy cohorts containing predicted TSNs for tumor neoantigen burden (TNB) with outcome association, the metrics were evaluated as TSNs prioritizers and as immunotherapy response biomarkers.

Results

Our results show high performance variability among methods, highlighting the need for substantial improvement. Deep learning predictors were top ranked on ITSNdb but show discrepancy on validation databases. In overall, current predicted TNB did not outperform existing biomarkers.

Conclusion

Recommendations for their clinical application and the ITSNdb are presented to promote development and comparison of computational TSNs immunogenicity predictors.

Immunosurveillance shapes the emergence of neo-epitope landscapes of sarcomas, revealing prime targets for immunotherapy

T cells recognize tumor-derived mutated peptides presented on MHC by tumors. The recognition of these neo-epitopes leads to rejection of tumors, an event that is critical for successful cancer immunosurveillance. Determination of tumor-rejecting neo-epitopes in human tumors has proved difficult, though recently developed systems approaches are becoming increasingly useful at evaluating their immunogenicity. We have used the differential aggretope index to determine the neo-epitope burden of sarcomas and observed a conspicuously titrated antigenic landscape, ranging from the highly antigenic osteosarcomas to the low antigenic leiomyosarcomas and liposarcomas. We showed that the antigenic landscape of the tumors inversely reflected the historical T cell responses in the tumor-bearing patients. We predicted that highly antigenic tumors with poor antitumor T cell responses, such as osteosarcomas, would be responsive to T cell-based immunotherapy regimens and demonstrated this in a murine osteosarcoma model. Our study presents a potentially novel pipeline for determining antigenicity of human tumors, provides an accurate predictor of potential neo-epitopes, and will be an important indicator of which cancers to target with T cell-enhancing immunotherapy.

Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology

Whole-genome sequencing either alone or in combination with whole-transcriptome sequencing has started to be used to analyze clinical tumor samples to improve diagnosis, provide risk stratification, and select patient-specific therapies. Compared with current genomic testing strategies, largely focused on small number of genes tested individually or targeted panels, whole-genome and transcriptome sequencing (WGTS) provides novel opportunities to identify and report a potentially much larger number of actionable alterations with diagnostic, prognostic, and/or predictive impact. Such alterations include point mutations, indels, copy- number aberrations and structural variants, but also germline variants, fusion genes, noncoding alterations and mutational signatures. Nevertheless, these comprehensive tests are accompanied by many challenges ranging from the extent and diversity of sequence alterations detected by these methods to the complexity and limited existing standardization in interpreting them. We describe the challenges of WGTS interpretation and the opportunities with comprehensive genomic testing.

Self-antigens, benign autoimmunity and type 1 diabetes: a beta-cell and T-cell perspective

PURPOSE OF REVIEW

Recent work using immunopeptidomics and deconvolution of the antigenic reactivity of islet-infiltrating CD8+ T cells has expanded our knowledge about the autoimmune target epitopes of type 1 diabetes. The stem-like properties of autoimmune CD8+ T cells have also been described. We here propose a possible link between these findings.

RECENT FINDINGS

Weak major histocompatibility complex (MHC)-binding epitopes list among the major targets of human islet-infiltrating CD8+ T cells, likely resulting in low peptide-MHC presentation that delivers weak T-cell receptor (TCR) signals, especially in the face of low-affinity autoimmune TCRs. These weak TCR signals may favor the maintenance of the partially differentiated stem-like phenotype recently described for islet-reactive CD8+ T cells in the blood and pancreatic lymph nodes. These weak TCR signals may also be physiological, reflecting the need for self-peptide-MHC contacts to maintain homeostatic T-cell survival and proliferation. These features may underlie the universal state of benign autoimmunity that we recently described, which is characterized by islet-reactive, naïve-like CD8+ T cells circulating in all individuals.

SUMMARY

These observations provide novel challenges and opportunities to develop circulating T-cell biomarkers for autoimmune staging. Therapeutic halting of islet autoimmunity may require targeting of stem-like T cells to blunt their self-regeneration.

Therapeutic cancer vaccines: reasons to believe

Our hopes of using the power of the immune system to control tumours have been partially fulfilled with anti-PD1 antibodies and other checkpoint inhibitors and the use of engineered T cells targeting lineage-specific surface markers with chimeric antigen receptors. Can these successes be generalised? Therapeutic cancer vaccines aim to educate or re-educate the immune system to recognise tumour specific or tumour associated antigens. After many false dawns, some positive data for the effectiveness of such an approach is starting to emerge in advanced solid tumours, albeit as combination therapies with checkpoint inhibitors. But is the field targeting the right antigens? Interventions using the most effective vaccine platforms to target certain sets of antigens in patients with low disease burden might bring impressive long-term benefits to patients as single agents.

Branca RM, Lehtiö J, Sikanen TM, Cerullo V. PeptiCHIP: A Microfluidic Platform for Tumor Antigen Landscape Identification

Identification of HLA class I ligands from the tumor surface (ligandome or immunopeptidome) is essential for designing T-cell mediated cancer therapeutic approaches. However, the sensitivity of the process for isolating MHC-I restricted tumor-specific peptides has been the major limiting factor for reliable tumor antigen characterization, making clear the need for technical improvement. Here, we describe our work from the fabrication and development of a microfluidic-based chip (PeptiCHIP) and its use to identify and characterize tumor-specific ligands on clinically relevant human samples. Specifically, we assessed the potential of immobilizing a pan-HLA antibody on solid surfaces via well-characterized streptavidin-biotin chemistry, overcoming the limitations of the cross-linking chemistry used to prepare the affinity matrix with the desired antibodies in the immunopeptidomics workflow. Furthermore, to address the restrictions related to the handling and the limited availability of tumor samples, we further developed the concept toward the implementation of a microfluidic through-flow system. Thus, the biotinylated pan-HLA antibody was immobilized on streptavidin-functionalized surfaces, and immune-affinity purification (IP) was carried out on customized microfluidic pillar arrays made of thiol-ene polymer. Compared to the standard methods reported in the field, our methodology reduces the amount of antibody and the time required for peptide isolation. In this work, we carefully examined the specificity and robustness of our customized technology for immunopeptidomics workflows. We tested this platform by immunopurifying HLA-I complexes from 1 × 10⁶ cells both in a widely studied B-cell line and in patients-derived ex vivo cell cultures, instead of 5 × 10⁸ cells as required in the current technology. After the final elution in mild acid, HLA-I-presented peptides were identified by tandem mass spectrometry and further investigated by in vitro methods. These results highlight the potential to exploit microfluidics-based strategies in immunopeptidomics platforms and in personalized immunopeptidome analysis from cells isolated from individual tumor biopsies to design tailored cancer therapeutic vaccines. Moreover, the possibility to integrate multiple identical units on a single chip further improves the throughput and multiplexing of these assays with a view to clinical needs.

An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection

Identification of neoepitopes that are effective in cancer therapy is a major challenge in creating cancer vaccines. Here, using an entirely unbiased approach, we queried all possible neoepitopes in a mouse cancer model and asked which of those are effective in mediating tumor rejection and, independently, in eliciting a measurable CD8 response. This analysis uncovered a large trove of effective anticancer neoepitopes that have strikingly different properties from conventional epitopes and suggested an algorithm to predict them. It also revealed that our current methods of prediction discard the overwhelming majority of true anticancer neoepitopes. These results from a single mouse model were validated in another antigenically distinct mouse cancer model and are consistent with data reported in human studies. Structural modeling showed how the MHC I-presented neoepitopes had an altered conformation, higher stability, or increased exposure to T cell receptors as compared with the unmutated counterparts. T cells elicited by the active neoepitopes identified here demonstrated a stem-like early dysfunctional phenotype associated with effective responses against viruses and tumors of transgenic mice. These abundant anticancer neoepitopes, which have not been tested in human studies thus far, can be exploited for generation of personalized human cancer vaccines.

Endotoxin contamination in ovalbumin as viewed from a nano-immunotherapy perspective

Ovalbumin (OVA) is a model antigen commonly incorporated in smartly designed nanoparticles for delivery into antigen-presenting cells (APC), aiming to investigate the immune activity and therapeutic efficacy of nanoparticles that contain immunoregulatory compounds. However, the immunoresponse observed in nano-immunotherapy may unexpectedly arise from endotoxin impurity of OVA in the nanoparticles. Literature review shows that most researchers did not notice the importance of endotoxin-free OVA when used in nano-immunotherapy studies. Concentration at as low as 5 μg/ml OVA from Sigma-Aldrich (contains 0.625 ng/ml endotoxin) was able to activate APC such as dendritic cells and macrophages. Here, we proposed that the endotoxin impurity in OVA or the finished nanoproducts should be determined by both Limulus Amebocyte Lysate (LAL) and cell-based assay, to ensure the endotoxin-free quality of the nanoparticles. The endotoxin in OVA can be removed by endotoxin removal column and phase separation methods and endotoxin-free OVA can be purchased. This perspective alerts the researchers of endotoxin impurity of OVA that may transfer into the finished nanoparticles and introduce an unfavorable immunoregulatory function with false-positive results. OVA with minimal endotoxin level should be used in nano-immunotherapy studies to accurately reflect the true effects of nanoparticles on the immune system. This article is categorized under: Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

The intrinsic immunogenic properties of cancer cell lines, immunogenic cell death, and how these influence host antitumor immune responses

Modern cancer therapies often involve the combination of tumor-directed cytotoxic strategies and generation of a host antitumor immune response. The latter is unleashed by immunotherapies that activate the immune system generating a more immunostimulatory tumor microenvironment and a stronger tumor antigen-specific immune response. Studying the interaction between antitumor cytotoxic therapies, dying cancer cells, and the innate and adaptive immune system requires appropriate experimental tumor models in mice. In this review, we discuss the immunostimulatory and immunosuppressive properties of cancer cell lines commonly used in immunogenic cell death (ICD) studies being apoptosis or necroptosis. We will especially focus on the antigenic component of immunogenicity. While in several cancer cell lines the epitopes of endogenously expressed tumor antigens are known, these intrinsic epitopes are rarely determined in experimental apoptotic or necroptotic ICD settings. Instead by far the most ICD research studies investigate the antigenic response against exogenously expressed model antigens such as ovalbumin or retroviral epitopes (e.g., AH1). In this review, we will argue that the immune response against endogenous tumor antigens and the immunopeptidome profile of cancer cell lines affect the eventual biological readouts in the typical prophylactic tumor vaccination type of experiments used in ICD research, and we will propose additional methods involving immunopeptidome profiling, major histocompatibility complex molecule expression, and identification of tumor-infiltrating immune cells to document intrinsic immunogenicity following different cell death modalities.

T-cell receptor affinity in the age of cancer immunotherapy

The strength of the interaction between T-cell receptors (TCRs) and their ligands, peptide/major histocompatibility complex complexes (pMHCs), is one of the most frequently discussed and investigated features of T cells in immuno-oncology today. Although there are many molecules on the surface of T cells that interact with ligands on other cells, the TCR/pMHC is the only receptor-ligand pair that offers antigen specificity and dictates the functional response of the T cell. The strength of the TCR/pMHC interaction, along with the environment in which this interaction takes place, is key to how the T cell will respond. The TCR repertoire of T cells that interact with tumor-associated antigens is vast, although typically of low affinity. Here, we focus on the low-affinity interactions between TCRs from CD8+ T cells and different models used in immuno-oncology.

Gene Therapy in Cancer Treatment: Why Go Nano?

The proposal of gene therapy to tackle cancer development has been instrumental for the development of novel approaches and strategies to fight this disease, but the efficacy of the proposed strategies has still fallen short of delivering the full potential of gene therapy in the clinic. Despite the plethora of gene modulation approaches, e.g., gene silencing, antisense therapy, RNA interference, gene and genome editing, finding a way to efficiently deliver these effectors to the desired cell and tissue has been a challenge. Nanomedicine has put forward several innovative platforms to overcome this obstacle. Most of these platforms rely on the application of nanoscale structures, with particular focus on nanoparticles. Herein, we review the current trends on the use of nanoparticles designed for cancer gene therapy, including inorganic, organic, or biological (e.g., exosomes) variants, in clinical development and their progress towards clinical applications.