Immunoprecipitation methods impact the peptide repertoire in immunopeptidomics

PCI-DB: a novel primary tissue immunopeptidome database to guide next-generation peptide-based immunotherapy development

BACKGROUND

Various cancer immunotherapies rely on the T cell-mediated recognition of peptide antigens presented on human leukocyte antigens (HLA). However, the identification and selection of naturally presented peptide targets for the development of personalized as well as off-the-shelf immunotherapy approaches remain challenging.

METHODS

Over 10,000 raw mass spectrometry (MS) files from over 3,000 tissue samples were analyzed, summing to approximately seven terabytes of data. The raw MS data were processed using the standardized and open-source nf-core pipelines MHCquant2 and epitopeprediction, providing a uniform procedure for data handling. A global false discovery rate was applied to minimize false-positive identifications.

RESULTS

Here, we introduce the open-access Peptides for Cancer Immunotherapy Database (PCI-DB, https://pci-db.org/), a comprehensive resource of immunopeptidome data originating from various malignant and benign primary tissues that provides the research community with a convenient tool to facilitate the identification of peptide targets for immunotherapy development. The PCI-DB includes >6.6 million HLA class I and >3.4 million HLA class II peptides from over 40 tissue types and cancer entities. First application of the database provided insights into the representation of cancer-testis antigens across malignant and benign tissues, enabling the identification and characterization of cross-tumor entity and entity-specific tumor-associated antigens (TAAs) as well as naturally presented neoepitopes from frequent cancer mutations. Further, we used the PCI-DB to design personalized peptide vaccines for two patients suffering from metastatic cancer. In a retrospective analysis, PCI-DB enabled the composition of both a multi-peptide vaccine comprising non-mutated, highly frequent TAAs matching the immunopeptidome of the individual patient's tumor and a neoepitope-based vaccine matching the mutational profile of a patient with cancer. Both vaccine approaches induced potent and long-lasting T-cell responses, accompanied by long-term survival of these patients with advanced cancer.

CONCLUSION

The PCI-DB provides a highly versatile tool to broaden the understanding of cancer-related antigen presentation and, ultimately, supports the development of novel immunotherapies.

Preparation and characterization of immunopeptides isolated from pig spleen and evaluation of their immunomodulatory properties in vitro and in vivo

The importance of small bioactive peptides derived from pig spleen have been used to enhance immune responses and support intestinal health. However, there is a lack of information regarding the conformational relationship and their effects on immune function of pig spleen proteins (PSPs). The objective of this study was to prepare and assess the immunomodulatory characteristics of immunopeptides from PSP. Firstly, enzymatic hydrolysates from PSP were prepared using alkaline protease and aminopeptidase, and small hydrolysate fractions with a <3 kDa were separated by SDS-PAGE and GPC. The bioactive peptides were then identified at peaks 5 to 7 (PSP-5, 6 and 7) by HPLC and TOF-MS, which were mainly composed of Pro-Glu-Leu by LC-MS. The PSP-5 and PSP-6 pronounced greater beneficial effects on cell viability and nitric oxide (NO) production than PSP-7 in macrophage, and PSP-5 exhibited a higher immunomodulatory ability than PSP-6. In vivo, the oral administration of 25-50 mg PSP-5/kg body weight (BW) protected against cyclophosphamide (CTX)-induced immunosuppression in spleen and intestine of mouse, as evidenced by increased cytokine and sIgA productions. In conclusion, a novel set of bioactive immunopeptides derived from PSP through enzymatic hydrolysis could enhance immunomodulatory properties.

Novel insights into TCR-T cell therapy in solid neoplasms: optimizing adoptive immunotherapy

Adoptive immunotherapy in the T cell landscape exhibits efficacy in cancer treatment. Over the past few decades, genetically modified T cells, particularly chimeric antigen receptor T cells, have enabled remarkable strides in the treatment of hematological malignancies. Besides, extensive exploration of multiple antigens for the treatment of solid tumors has led to clinical interest in the potential of T cells expressing the engineered T cell receptor (TCR). TCR-T cells possess the capacity to recognize intracellular antigen families and maintain the intrinsic properties of TCRs in terms of affinity to target epitopes and signal transduction. Recent research has provided critical insight into their capability and therapeutic targets for multiple refractory solid tumors, but also exposes some challenges for durable efficacy. In this review, we describe the screening and identification of available tumor antigens, and the acquisition and optimization of TCRs for TCR-T cell therapy. Furthermore, we summarize the complete flow from  laboratory to clinical applications of TCR-T cells. Last, we emerge future prospects for improving therapeutic efficacy in cancer world with combination therapies or TCR-T derived products. In conclusion, this review depicts our current understanding of TCR-T cell therapy in solid neoplasms, and provides new perspectives for expanding its clinical applications and improving therapeutic efficacy.