Pipeline to identify neoantigens exposed by radiation.

Mutation-associated neoantigens are key targets of tumor-specific T cells and thus play a major role in driving responses to immune checkpoint blockade (ICB) therapy in tumors with high mutational burden. However, only a small number of mutated peptides are actually presented by MHC molecules and only a minority can induce T cell responses. In addition, the recognition of these neoantigens by T cells is limited by the level of expression of the mutated gene product in the tumor cells. Preclinical studies have shown that radiation can convert the irradiated tumor into an in situ vaccine, leading to the priming of tumor-specific T cells and to the rejection of otherwise ICB-resistant tumors. There is now preclinical and clinical evidence that radiation can upregulate the expression of genes containing immunogenic mutations and expose them to the immune system. Therefore, the identification of neoantigens upregulated by radiation could help to predict which patients might benefit from treatment with combinations of radiotherapy and ICB and could also be incorporated into personalized neoantigen vaccination strategies. In this chapter, we present the pipeline that we used to identify relevant radiation-upregulated neoantigens in a poorly immunogenic mouse model of metastatic breast cancer.

Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication.

Multiple coronaviruses have emerged independently in the past 20 years that cause lethal human diseases. Although vaccine development targeting these viruses has been accelerated substantially, there remain patients requiring treatment who cannot be vaccinated or who experience breakthrough infections. Understanding the common host factors necessary for the life cycles of coronaviruses may reveal conserved therapeutic targets. Here, we used the known substrate specificities of mammalian protein kinases to deconvolute the sequence of phosphorylation events mediated by three host protein kinase families (SRPK, GSK-3, and CK1) that coordinately phosphorylate a cluster of serine and threonine residues in the viral N protein, which is required for viral replication. We also showed that loss or inhibition of SRPK1/2, which we propose initiates the N protein phosphorylation cascade, compromised the viral replication cycle. Because these phosphorylation sites are highly conserved across coronaviruses, inhibitors of these protein kinases not only may have therapeutic potential against COVID-19 but also may be broadly useful against coronavirus-mediated diseases.

Raman spectroscopy and supervised learning as a potential tool to identify high-dose-rate-brachytherapy induced biochemical profiles of prostate cancer.

High-dose-rate-brachytherapy (HDR-BT) is an increasingly attractive alternative to external beam radiation-therapy for patients with intermediate risk prostate cancer. Despite this, no bio-marker based method currently exists to monitor treatment response, and the changes which take place at the biochemical level in hypo-fractionated HDR-BT remain poorly understood. The aim of this pilot study is to assess the capability of Raman spectroscopy (RS) combined with principal component analysis (PCA) and random-forest classification (RF) to identify radiation response profiles after a single dose of 13.5 Gy in a cohort of nine patients. We here demonstrate, as a proof-of-concept, how RS-PCA-RF could be utilised as an effective tool in radiation response monitoring, specifically assessing the importance of low variance PCs in complex sample sets. As RS provides information on the biochemical composition of tissue samples, this technique could provide insight into the changes which take place on the biochemical level, as result of HDR-BT treatment.

Radiation therapy-induced remodeling of the tumor immune microenvironment.

The tumor immune microenvironment is a determinant of response to cancer immunotherapy and, in many cases, is prognostic for patient survival independently of the type of treatment. Radiation therapy is used in most cancer patients for its direct cytotoxic effects on malignant cells but there is increasing evidence that it also reprograms the tumor immune microenvironment. In this review we discuss the main mechanisms whereby the local inflammatory reaction induced by radiation can reset the cross-talk between the tumor and the immune system. The outcome reflects the balance between immunostimulatory signals that lead to increased tumor antigen presentation and effector T cell activation, and immunosuppressive signals that hinder radiation-induced tumor rejection. The emerging role of small extracellular vesicles (exosomes) in this process will be discussed. Overall, preclinical and early clinical findings support the hypothesis that radiation has the potential to generate an immune-permissive tumor microenvironment. An improved understanding of the pathways involved will enable the design of more effective combinations of radiation and immunotherapy, based on a rationale integration of radiation with other interventions.

Expression of the mono-ADP-ribosyltransferase ART1 by tumor cells mediates immune resistance in non-small cell lung cancer.

Most patients with non-small cell lung cancer (NSCLC) do not achieve durable clinical responses from immune checkpoint inhibitors, suggesting the existence of additional resistance mechanisms. Nicotinamide adenine dinucleotide (NAD)-induced cell death (NICD) of P2X7 receptor (P2X7R)-expressing T cells regulates immune homeostasis in inflamed tissues. This process is mediated by mono-adenosine 5'-diphosphate (ADP)-ribosyltransferases (ARTs). We found an association between membranous expression of ART1 on tumor cells and reduced CD8 T cell infiltration. Specifically, we observed a reduction in the P2X7R+ CD8 T cell subset in human lung adenocarcinomas. In vitro, P2X7R+ CD8 T cells were susceptible to ART1-mediated ADP-ribosylation and NICD, which was exacerbated upon blockade of the NAD+-degrading ADP-ribosyl cyclase CD38. Last, in murine NSCLC and melanoma models, we demonstrate that genetic and antibody-mediated ART1 inhibition slowed tumor growth in a CD8 T cell-dependent manner. This was associated with increased infiltration of activated P2X7R+CD8 T cells into tumors. In conclusion, we describe ART1-mediated NICD as a mechanism of immune resistance in NSCLC and provide preclinical evidence that antibody-mediated targeting of ART1 can improve tumor control, supporting pursuit of this approach in clinical studies.

Raman spectroscopy detects metabolic signatures of radiation response and hypoxic fluctuations in non-small cell lung cancer.

BACKGROUND: Radiation therapy is a standard form of treating non-small cell lung cancer, however, local recurrence is a major issue with this type of treatment. A better understanding of the metabolic response to radiation therapy may provide insight into improved approaches for local tumour control. Cyclic hypoxia is a well-established determinant that influences radiation response, though its impact on other metabolic pathways that control radiosensitivity remains unclear. METHODS: We used an established Raman spectroscopic (RS) technique in combination with immunofluorescence staining to measure radiation-induced metabolic responses in human non-small cell lung cancer (NSCLC) tumour xenografts. Tumours were established in NOD.CB17-Prkdcscid/J mice, and were exposed to radiation doses of 15 Gy or left untreated. Tumours were harvested at 2 h, 1, 3 and 10 days post irradiation. RESULTS: We report that xenografted NSCLC tumours demonstrate rapid and stable metabolic changes, following exposure to 15 Gy radiation doses, which can be measured by RS and are dictated by the extent of local tissue oxygenation. In particular, fluctuations in tissue glycogen content were observed as early as 2 h and as late as 10 days post irradiation. Metabolically, this signature was correlated to the extent of tumour regression. Immunofluorescence staining for γ-H2AX, pimonidazole and carbonic anhydrase IX (CAIX) correlated with RS-identified metabolic changes in hypoxia and reoxygenation following radiation exposure. CONCLUSION: Our results indicate that RS can identify sequential changes in hypoxia and tumour reoxygenation in NSCLC, that play crucial roles in radiosensitivity.

Haralick texture feature analysis for quantifying radiation response heterogeneity in murine models observed using Raman spectroscopic mapping.

Tumour heterogeneity plays a large role in the response of tumour tissues to radiation therapy. Inherent biological, physical, and even dose deposition heterogeneity all play a role in the resultant observed response. We here implement the use of Haralick textural analysis to quantify the observed glycogen production response, as observed via Raman spectroscopic mapping, of tumours irradiated within a murine model. While an array of over 20 Haralick features have been proposed, we here concentrate on five of the most prominent features: homogeneity, local homogeneity, contrast, entropy, and correlation. We show that these Haralick features can be used to quantify the inherent heterogeneity of the Raman spectroscopic maps of tumour response to radiation. Furthermore, our results indicate that Haralick-calculated textural features show a statistically significant dose dependent variation in response heterogeneity, specifically, in glycogen production in tumours irradiated with clinically relevant doses of ionizing radiation. These results indicate that Haralick textural analysis provides a quantitative methodology for understanding the response of murine tumours to radiation therapy. Future work in this area can, for example, utilize the Haralick textural features for understanding the heterogeneity of radiation response as measured by biopsied patient tumour samples, which remains the standard of patient tumour investigation.

Breast cancer subtype specific biochemical responses to radiation.

External beam radiotherapy is a common form of treatment for breast cancer. Among patients and across different breast cancer subtypes, the response to radiation is heterogeneous. Radiation-induced biochemical changes were examined by Raman spectroscopy using cell lines that represent a spectrum of human breast cancer. Principal component analysis (PCA) and partial least squares discriminant analysis (PLSDA) revealed unique Raman spectral features in the HER2 and Ki67 subtype. The changes in Raman spectral profiles to different doses of radiation (0-50 Gy) included variations in the levels of proteins, lipids, nucleic acids and glycogen. Importantly, the differences in radiation-induced changes on the normal breast epithelial cell line MCF10A could be discriminated within and across the various breast tumor cell lines. These results demonstrate a novel approach to uncover differences between breast cancer cell subtypes and surrounding normal tissues by their biochemical variations in response to radiation.

Raman Spectroscopic Signatures Reveal Distinct Biochemical and Temporal Changes in Irradiated Human Breast Adenocarcinoma Xenografts.

Radiation therapy plays a crucial role in the management of breast cancer. However, current standards of care have yet to accommodate patient-specific radiation sensitivity. Raman spectroscopy is promising for applications in radiobiological studies and as a technique for personalized radiation oncology, since it can detect spectral changes in irradiated tissues. In this study, we used established Raman spectroscopic approaches to investigate the biochemical nature and temporal evolution of spectral changes in human breast adenocarcinoma xenografts after in vivo irradiation. Spectral alterations related to cell cycle variations with radiation dose were identified for tumors treated using a range of single-fraction ionizing radiation doses. Additional dose-dependent spectral changes linked to specific proteins, nucleic acids and lipids were also identified in irradiated tumors with a clear temporal evolution of the expression of these signatures. This study reveals distinct shifts in Raman spectra after in vivo irradiation of human breast adenocarcinoma xenografts, emphasizing the significance of Raman spectroscopy for assessing tumor response during radiation therapy.