Endogenous viral elements constitute a complementary source of antigens for personalized cancer immunotherapy
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE223515 | GEO | 2025/03/26
REPOSITORIES: GEO
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Project description:Endogenous viral elements constitute a complementary source of antigens for personalized cancer immunotherapy
| PRJNA926630 | ENA
Project description:Patients with glioblastoma (GB) so far do not sufficiently benefit from recent breakthroughs with checkpoint inhibitors (CPI), for which high mutational load and responses to neo-epitopes are regarded essential. GB tumours show limited intra-tumoral immune cell infiltration and carry 30-50 non-synonymous mutations only. Exploitation of the full repertoire of tumour antigens - non-mutated and neo-epitopes – may offer more effective immunotherapies, especially for tumours with low mutational load. In the first-in-human trial GAPVAC-101, the Glioma Actively Personalized Vaccine Consortium (GAPVAC) integrated both tracks highly individualized into standard treatment to optimally exploit the limited target space for patients with newly diagnosed GB. Fifteen HLA-A*02:01+ or -A*24:02+ patients were treated with a warehouse-based vaccine (APVAC1) targeting non-mutated antigens followed by APVAC2, targeting preferentially neo-epitopes. Personalization was based on mutations, transcriptome, and immunopeptidome of the individual tumours. The GAPVAC approach was feasible and vaccinations adjuvanted by poly-ICLC and GM-CSF displayed favourable safety and excellent immunogenicity: Non-mutated APVAC1 antigens induced sustained central memory CD8+ T-cell responses. APVAC2 induced predominantly TH1 CD4+ T-cell responses against predicted neo-epitopes. www.GAPVAC.eu
2018-11-15 | GSE122498 | GEO
Project description:Cytotoxic T-lymphocyte associated antigen-4 (CTLA-4) and Programmed death-1 (PD-1) are immunoregulatory receptors expressed on T cells that play important roles in suppressing immune responses to cancer. Although monoclonal antibodies that target CTLA-4 or PD-1 stimulate therapeutic anti-tumour T cell responses, the tumour antigens recognized by checkpoint blockade immunotherapy remain undefined. Herein, we use genomics and bioinformatics approaches to identify tumour-specific mutant proteins as a major class of T cell rejection antigens following αPD-1 and/or αCTLA-4 treatment of mice bearing progressively growing sarcomas. We validate this conclusion by showing that (a) the predicted mutant epitopes associate with MHC class I molecules of the tumour; (b) T cells specific for these mutant epitopes infiltrate tumours; and (c) therapeutic vaccines incorporating these mutant epitopes induce tumour rejection comparably to checkpoint blockade immunotherapy. Whereas, T cells with the same antigen specificity are present in progressively growing tumours in control mice, tumour-specific T cells in αPD-1- and/or αCTLA-4-treated mice express some overlapping but mostly treatment-specific transcriptional profiles that render them capable of tumour rejection. Thus, tumour-specific mutant antigens are not only important targets of checkpoint blockade therapy but also can be used to identify tumour antigen-specific T cells that function as biomarkers of successful anti-tumour responses.
2014-11-07 | GSE62771 | GEO
Project description:E-cigarette use (vaping) has become widespread, and its effects on airway inflammation and disease are not fully delineated. E-cigarette vapor extract (EVE) profoundly affects neutrophil function. We hypothesized that EVE also alters eosinophil function and thus could impact allergic airways disease. We employed RNA-sequencing to measure the ex vivo effect of EVE components on human eosinophil transcription. Eosinophils from 7 non-vaping subjects without asthma were isolated by negative selection from venous blood. Cells were incubated for 48 hours with EVE consisting of glycerin, propylene glycol and nicotine (EVE+), EVE without nicotine (“EVE-”), Extract Buffer (EB), and untreated media. Bulk RNA-sequencing was performed. Principal component analysis revealed that the EVE+ and EVE- conditions clustered closely together. Differential gene expression analysis revealed a “negative regulation of interferon gamma production” and “apoptotic mitochondrial changes” pathways for genes upregulated in EVE- samples and a down regulation of “inflammatory response” and “chemokine signaling” in comparison to the EB control condition. 93 genes were differentially expressed genes between EVE+ and EVE-, indicating a relatively small effect of nicotine on eosinophil gene expression. These results demonstrate that EVE significantly alters eosinophil gene expression, predominantly mediated by propylene glycol and glycerin rather than by nicotine. This study motivates further research into the pathogenic effects of vaping on airway eosinophils and allergic airways disease.
2025-04-09 | GSE263814 | GEO
Project description:To elucidate the T cell epitopes of SARS-CoV-2, we stimulated human PBMCs from healthy donors and convalescent COVID-19 patients with various SARS-CoV-2 antigens, sorted the activated T cells and performed sc-RNA and -TCR sequencing. We obtained thousands of T cell clonotypes that responded to SARS-CoV-2 antigens, and identified the epitopes and restricting HLAs of several clonotypes that were significantly expanded in the COVID-19 patients.
2021-10-07 | GSE184806 | GEO
Project description:The chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses the Drosophila even skipped (eve) gene is formed by the head-to-tail pairing of the nhomie and homie boundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked the nhomie boundary region with two attP sites. The attP sites were then used to generate four boundary replacements: λ DNA, nhomie forward (WT orientation), nhomie reverse (opposite of WT), and homie forward (same as WT homie). The nhomie forward replacement restores the WT physical and regulatory landscape: In MicroC experiments, the eve TAD is a volcano triangle topped by a plume, and the eve gene and its regulatory elements are sequestered from interactions with neighbors. The λ DNA replacement lacks boundary function: the endpoint of the “new” eve TAD on the nhomie side is ill-defined, and eve stripe enhancers activate a nearby gene, eIF3j. While nhomie reverse and homie forward restore the eve TAD, the topology is a circle-loop, and this changes the local physical and regulatory landscape. In MicroC experiments, the eve TAD interacts with its neighbors, and the plume at the top of the eve volcano triangle is replaced by a cloud of contacts with the next-door TADs. Consistent with the loss of isolation afforded by the stem-loop topology, the eve enhancers weakly activate genes in the neighboring TADs. Conversely, eve function is partially disrupted.
2024-04-04 | GSE263270 | GEO
Project description:Spindle assembly and function require precise control of microtubule nucleation and dynamics. The chromatin-driven spindle assembly pathway exerts such control locally in the vicinity of chromosomes. One of the key targets of this pathway is TPX2. The molecular mechanism of how TPX2 stimulates microtubule nucleation is not understood. Using microscopy-based dynamic in vitro reconstitution assays with purified proteins, we find that human TPX2 directly stabilizes growing microtubule ends and stimulates microtubule nucleation by stabilizing early microtubule nucleation intermediates. Human microtubule polymerase chTOG (XMAP215/Msps/Stu2p/Dis1/Alp14 homologue) only weakly promotes nucleation, but acts synergistically with TPX2. Hence, a combination of distinct and complementary activities is sufficient for efficient microtubule formation in vitro. Importins control the efficiency of the microtubule nucleation by selectively blocking the interaction of TPX2 with microtubule nucleation intermediates. This in vitro reconstitution reveals the molecular mechanism of regulated microtubule formation by a minimal nucleation module essential for chromatin-dependent microtubule nucleation in cells.
| S-EPMC4826748 | biostudies-literature
Project description:Wild Asparagus shoots are consumed worldwide, although most species remain understudied. In this work, a total of four wild Asparagus species were collected from different locations and analyzed compared with farmed A. officinalis. Shoots were screened for (i) phenolic compounds by HPLC-DAD and LC-MS; (ii) total phenolic acids and total flavonoid content by the Folin-Ciocalteu and aluminum chloride methods; (iii) vitamin C by HPLC-DAD; (iv) antioxidant activity by the DPPH and ABTS•+ methods; and (v) the in vitro antiproliferative activities against HT-29 colorectal cancer cells by the MTT assay. Phenolics ranged from 107.5 (A. aphyllus) to 605.4 mg/100 g dry weight (dw) (A. horridus). Vitamin C ranged from 15.8 (A. acutifolius) to 22.7 mg/100 g fresh weight (fw) (A. officinalis). The antioxidant activity was similar in all species, standing out in A. officinalis with 5.94 (DPPH) and 4.64 (ABTS) mmol TE/100 g dw. Among phenolics, rutin reached the highest values (574 mg/100 g dw in A. officinalis), followed by quercetin, nicotiflorin, asterin, and narcissin. The MTT assay revealed the inhibitory effects of ethanol extracts against HT-29 cancer cells, highlighting the cell growth inhibition exercised by A. albus (300 µg/mL after 72 h exposure to cells). This work improves knowledge on the phytochemicals and bioactivities of the shoots of wild Asparagus species and confirms their suitability for use as functional foods.
| S-EPMC10421306 | biostudies-literature
Project description:Seeds of most Arecaceae species are an underutilized raw material that can constitute a source of nutritionally relevant compounds. In this work, seeds of 24 Arecaceae taxa were analyzed for fatty acids (FAs) by GC-FID, for phenolics by HPLC-DAD and LC-MS, and for their antitumor activity against the HT-29 colorectal cancer cell line by the MTT assay. Lauric, oleic, and linoleic acids were the prominent FAs. Cocoseae species contained total FAs at 28.0-68.3 g/100 g seeds, and in other species total FAs were from 1.2 (Livistona saribus) to 9.9 g/100 g (Washingtonia robusta). Sabal domingensis, Chamaerops humilis, and Phoenix dactylifera var. Medjool had unsaturated/saturated FA ratios of 1.65, 1.33-1.78, and 1.31, respectively, and contained 7.4, 5.5-6.3, and 6.4 g FAs/100 g seeds, respectively. Thus, they could be used as raw materials for healthy oilseed production. Phenolics ranged between 39 (Livistona fulva) and 246 mg/100 g (Sabal palmetto), and of these, caffeic acid, catechin, dactylifric acid, and rutin had the highest values. (-)-Epicatechin was identified in most seed extracts by LC-MS. Hydroalcoholic extracts from five species showed a dose-dependent inhibitory effect on HT-20 cells growth at 72 h (GI50 at 1533-1968 µg/mL). Overall, Arecaceae seeds could be considered as a cheap source of health-promoting compounds.
| S-EPMC9867020 | biostudies-literature
Project description:Combining multiple therapeutic strategies in NRAS/BRAF mutant melanoma – namely MEK/BRAF kinase inhibitors, immune checkpoint inhibitors, and targeted immunotherapies – may offer an improved survival benefit by overcoming limitations associated with any individual therapy. Still, optimal combination, order, and timing of administration remains under investigation. Here, we measure how MEK inhibition alters anti-tumor immunity by utilizing quantitative immunopeptidomics to profile changes the peptide MHC (pMHC) repertoire. These data reveal a collection of tumor antigens whose presentation levels are selectively augmented following therapy, including several epitopes present at over 1000 copies-per-cell. We leveraged the tunable abundance of MEKi-modulated antigens by targeting 4 epitopes with pMHC-specific T cell engagers and antibody drug conjugates, enhancing cell killing in tumor cells following MEK inhibition. These results highlight drug treatment as a means to enhance immunotherapy efficacy by targeting specific upregulated pMHCs and provide a methodological framework for identifying, quantifying, and therapeutically targeting additional epitopes of interest.
2022-11-15 | GSE185284 | GEO