Immunospot Assessment of T-Cell Responses in Preclinical Tumor Models with Undefined Target Antigens

Assessment of functional tumor-specific T-cell responses in preclinical tumor models represents an important tool for successful translation of new immunotherapies to clinics. Usually, it requires a known tumor antigen target. Here, we describe the method to detect tumor-specific T cell after immunotherapies without a known antigen. Splenocytes, lymph node immune cells, or PBMCs are isolated from treated mice and stimulated with relevant tumor cells ex vivo before immunospot analysis of Granzyme B and interferon γ-positive T cells. The method is especially valuable for monitoring tumor-specific T cells after vaccination with various whole tumor vaccines or after in situ vaccination and other antigen agnostic immunotherapies, where no specific antigens are used.

Development of Clinical-Grade Antibodies against Tumor-Specific Mutations to Target Neuroblastoma

OBJECTIVE

Tumor heterogeneity is a fundamental problem in treating cancer with monotargeting therapy, including chemical, antibody, and T cell therapies. Our goal is to target multiple mutated peptides found in a patient's cancer to increase antibody therapy effectiveness.

METHODS

Tumor samples were derived from patients with neuroblastoma. Whole-exome sequencing was performed of tumor and normal cells. Mutated proteins with missense mutations were selected from the patient tumor. These mutated proteins were further selected for the presence of missense mutations in the outer cell surface. Peptides representing a mutated section of the proteins were used for vaccinating rabbits and generating anti-peptide antibodies. The binding of individual polyclonal antibodies (pAbs) and the mixtures of pAbs were determined against the patient's tumor as cultured neuroblastoma cells and in a murine xenograft model. Antibodies were prepared according to FDA requirements of a phase I clinical protocol.

RESULTS

All of the generated rabbit pAbs bound with high affinity to the corresponding peptide used for vaccination. The pAbs also bound to low passage neuroblastoma cells. Mixed as cocktails, the pAbs had substantially increased binding to cells and bound well to the xenograft tissue. No binding was observed to the panel of normal human tissues. Preparation of pAbs by an academic lab to clinical-grade was approved by FDA for phase I clinical trial.

CONCLUSION

We describe a new strategy to make customized antibodies for individual cancer patients and present the data required to meet FDA specifications to begin a phase I clinical trial.

Genome-wide DNA methylation profiling and identification of potential pan-cancer and tumor-specific biomarkers

DNA methylation alterations have already been linked to cancer, and their usefulness for therapy and diagnosis has encouraged research into the human epigenome. Several biomarker studies have focused on identifying cancer types individually, yet common cancer and multi-cancer markers are still underexplored. We used The Cancer Genome Atlas (TCGA) to investigate genome-wide methylation profiles of 14 different cancer types and developed a three-step computational approach to select candidate biomarker CpG sites. In total, 1,991 pan-cancer and between 75 and 1,803 cancer-specific differentially methylated CpG sites were discovered. Differentially methylated blocks and regions were also discovered for the first time on such a large-scale. Through a three-step computational approach, a combination of four pan-cancer CpG markers was identified from these sites and externally validated (AUC = 0.90), maintaining comparable performance across tumor stages. Additionally, 20 tumor-specific CpG markers were identified and made up the final type-specific prediction model, which could accurately differentiate tumor types (AUC = 0.87-0.99). Our study highlights the power of the methylome as a rich source of cancer biomarkers, and the signatures we identified provide a new resource for understanding cancer mechanisms on the wider genomic scale with strong applicability in the context of new minimally invasive cancer detection assays.

Acid-triggered degradable diblock poly(doxorubicin)-polyethylene glycol polyprodrug with doxorubicin as structural unit for tumor intracellular delivery

Polyprodrugs, in which drug was used as the structural unit by linking with each other via the dynamic covalent bonds in the main chain, are expected to endow excellent drug delivery performance. Here, acid-triggered degradable diblock polyprodrug, poly(doxorubicin)-polyethylene glycol (PDOX-PEG), was designed with DOX as structural unit alternately linked with acid-labile hydrazone and maleic amide groups, by the polycondensation of DOX-based dimers (D-DOX_ADH or D-DOX_MAH) with PEGylated dimer (DOX-ADH-DOX-PEG) as end capping agent. The optimized PDOX-PEG, which was synthesized with D-DOX_ADH and the PEGylated dimer at a feeding ratio of 10%, possessed a high M_n of 3.1 × 10⁴ g/mol with a high DOX content of 75.42%. It could easily self-assemble into near spherical nanoparticles with average hydrodynamic diameter of 135 nm. They showed excellent pH-triggered sustained drug release owing to the acid-triggered degradation of the polyprodrug block in the tumor intracellular microenvironment, with low premature drug leakage of 4.39 % within 60 h. The MTT results indicated the enhanced antitumor efficacy of the proposed PDOX-PEG nanoparticles than free DOX. The results demonstrated the promising potential of the proposed acid-triggered degradable diblock PDOX-PEG polyprodrug for tumor treatment.

Tumor-specific fluorescent Cdots-based nanotheranostics by acid-labile conjugation of doxorubicin onto reduction-cleavable Cdots-based nanoclusters

Carbon quantum dots (Cdots) have attracted more and more interests in bioimaging and tumor theranostics. However, their practical application has been limited due to the small particle size and non-tumor-specific fluorescence. Here, reduction-cleavable disulfide-linked Cdots-based nanoclusters were fabricated to conjugate doxorubicin (DOX) via an acid-labile hydrazone bond. Owing to the pH and reduction dual-stimuli responsiveness, the proposed Cdots-based nanotheranostics possessed unique tumor-specific fluorescent property and tumor-specific controlled drug release performance, indicating their promising potential for the in-situ real-time fluorescent monitoring of therapeutic response in future tumor therapy.

A cocktail of polyclonal affinity enriched antibodies against melanoma mutations increases binding and inhibits tumor growth

BACKGROUND

Antibodies that target a single tumor antigen fail to cure stage IV cancer patients due to tumor heterogeneity and variable expression of antigen. Tumor cells with insufficient binding of antibody will not undergo antibody induced cytotoxicity. We describe targeting multiple tumor-specific antigens that resulted in homogeneous dense binding to mouse melanoma cells and significant tumor growth inhibition.

METHODS

Surface-related tumor-specific mutations on B16-F10 cells were identified. Peptides containing the single amino acid mutation were synthesized for 9 different neoantigens. Rabbits were vaccinated with each of these peptides and high affinity polyclonal antibodies to each peptide were obtained. The 9 antibodies were combined as a cocktail and mice with implanted B16-F10 cells were treated with and without PD1 inhibitor.

RESULTS

Even a single dose of the antibody cocktail inhibited tumor growth and prolonged survival. PD1 inhibitor alone had little effect on tumor growth. The antibody cocktail plus PD1 inhibition increased tumor response and 4 doses of the cocktail completely prevented tumor growth in 50% of the mice. Complete responses were durable. The complete responders were highly resistant to tumor re-challenge at 6 months. No adverse events were identified in the antibody treated mice.

CONCLUSIONS

Multiple tumor-specific cell surface-related neoantigens were abundant in B16-F10 cells. Antibodies to 9 of these neoantigens had variable binding but when combined had dense homogeneous binding. Even one dose of this cocktail of 9 antibodies improved survival and when multiple doses were combined with PD1 inhibition 50% of the mice were rendered permanently tumor free.

Genome-wide isoform-level analysis reveals tumor-specific isoforms for lung adenocarcinoma diagnosis and prognosis

Last decades have witnessed the great progress in exploration of tumor transcriptome. However, most researches were restricted in gene-level expression. mRNA isoforms, especially tumor-specific isoforms have not been fully explored in tumor. Here, by analyzing RNA-seq data derived from hundreds of samples in TCGA projects, we comprehensively characterized the expression variations of mRNA isoforms in adenocarcinoma of lung (LUAD), which is one of leading causes of cancer-related death. Our analysis found that a variety of mRNA isoforms showed differential expression in LUAD tumor samples. Some of them even showed distinct variations compared to their host genes. Further analysis of functional enrichment revealed that up- and down-regulated mRNA isoforms took part in different types of biological process. In addition, we also identified hundreds of isoforms that expressed exclusively in LUAD tumor samples. Furthermore, the expression level of several isoforms, such as uc001kuk.3 and uc003yls.2, could separate tumor patients by overall survival periods. Our study provided new candidates for the diagnosis and prognosis of lung cancer.

Novel dual-mode nanobubbles as potential targeted contrast agents for female tumors exploration

The purpose of this study was to prepare tumor-specific dual-mode nanobubbles as both ultrasound contrast agents (UCAs) and near-infrared fluorescence (NIRF) imaging agents for female tumors. Recent studies have demonstrated the conjugation of anti-tumor ligands on the surface of nanobubbles for use as molecule-targeting ultrasound contrast agents for tumor visualization. However, this complicated procedure has also posed a challenge to nanobubble stability. Thus, in the present study, we combined the fluorescent dye, NIRF IR-780 iodide, which has lipid solubility and tumor-targeting characteristics, with the phospholipid film of nanobubbles that we constructed. We then characterized the physical features of the IR-780-nanobubbles, observed their tumor-targeting capacity in multiple female tumor cell types in vitro, and verified their capability for use in tumor-specific ultrasound contrast imaging and NIRF imaging in vivo. The results showed that the new IR-780-nanobubbles had a uniform nano-size (442.5 ± 48.6 nm) and stability and that they were safe and effective at NIRF imaging and ultrasound imaging in vitro. The IR-780-nanobubbles were found to automatically accumulate on different female tumor cells in vitro with a considerable targeting rate (close to 40 %) but did not accumulate on cardiac muscle cells used as a negative control. Importantly, the IR-780-nanobubbles can detect female tumors precisely via dual-mode imaging in vivo. In conclusion, the new dual-mode IR-780-nanobubbles are stable and have potential advantages in non-invasive tumor-specific detection for female tumors via contrast-enhanced ultrasound and NIRF imaging.