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Although most characterized tumor antigens are encoded by canonical transcripts (such as differentiation or tumor-testis antigens) or mutations (both driver and passenger mutations), recent results have shown that noncanonical transcripts including long noncoding RNAs and transposable elements (TEs) can also encode tumor-specific neo-antigens. Here, we investigate the presentation and immunogenicity of tumor antigens derived from noncanonical mRNA splicing events between coding exons and TEs. Comparing human non–small cell lung cancer (NSCLC) and diverse healthy tissues, we identified a subset of splicing junctions that is both tumor specific and shared across patients. We used HLA-I peptidomics to identify peptides encoded by tumor-specific junctions in primary NSCLC samples and lung tumor cell lines. Recurrent junction-encoded peptides were immunogenic in vitro, and CD8 + T cells specific for junction-encoded epitopes were present in tumors and tumor-draining lymph nodes from patients with NSCLC. We conclude that noncanonical splicing junctions between exons and TEs represent a source of recurrent, immunogenic tumor-specific antigens in patients with NSCLC.

Oncogenesis often implicates epigenetic alterations, including derepression of transposable elements (TEs) and defects in alternative splicing. Here, we explore the possibility that noncanonical splice junctions between exons and TEs represent a source of tumor-specific antigens. We show that mouse normal tissues and tumor cell lines express wide but distinct ranges of mRNA junctions between exons and TEs, some of which are tumor specific. Immunopeptidome analyses in tumor cell lines identified peptides derived from exon-TE splicing junctions associated to MHC-I molecules. Exon-TE junction–derived peptides were immunogenic in tumor-bearing mice. Both prophylactic and therapeutic vaccinations with junction-derived peptides delayed tumor growth in vivo. Inactivation of the TE-silencing histone 3–lysine 9 methyltransferase Setdb1 caused overexpression of new immunogenic junctions in tumor cells. Our results identify exon-TE splicing junctions as epigenetically controlled, immunogenic, and protective tumor antigens in mice, opening possibilities for tumor targeting and vaccination in patients with cancer.

Murine double minute 2 (Mdm2) is an E3 ubiquitin ligase that promotes cell growth through negative regulation of the tumour suppressor p53. Its blockade with the small molecule antagonist Nutlin-3a is currently tested on clinical trials for its potential benefit as cancer treatment. The crucial equilibrium between p53 and Mdm2 in the cell homeostasis raises however concern on the effect of this drug in healthy tissues. Its administration in a mouse AKI model showed a diminished capacity of healing and the specific deletion of Mdm2 in both podocytes and tubular cells induced p53-overexpression dependent cell death (podoptosis). For this reason we hypothesized that the administration of Nutlin-3a to healthy mice damages renal function by promoting podoptosis in podocytes and tubular cells. Consistent with the hypothesis, we observed that stimulation with Nutlin-3a increased cell death in cultured mouse podocytes and tubular cells. In addition, treatment with Nutlin-3a caused in healthy mice stabilization of p53 levels and subsequent podocytopenia, promoting albuminuria and impaired glomerular filtration barrier. Moreover, increased macrophage infiltration was observed together with upregulation of inflammatory and tubular injury markers and augmented blood urea nitrogen levels. Therefore, renal damage after blockade of Mdm2 needs to be regarded when considering Nutlin-3a therapy. As blockade of Mdm2 can at the same time be beneficial in chronic glomerulopathies by inhibiting podocyte mitotic catastrophe, we hypothesized that Nutlin-3a could ameliorate diabetic nephropathy by preventing mitotic catastrophe and inhibiting inflammation; effect that has been previously observed in different disease models, where inflammation plays a central role in the pathogenesis. The administration of Nutlin-3a to diabetic mice did indeed decrease inflammation and fibrosis but it did not improve podocyte injury or renal function; contrary to the original hypothesis, increased podocytopenia and decreased renal function in terms of BUN compared to the placebo group. These results could further support a recent work on metabolomics and computational network analysis from Saito et al., where Mdm2 was revealed as a relevant downregulated protein in the diabetic kidney disease. In conclusion, therapeutic Mdm2 blockade may hold the risk of damaging renal function in patients with no underlying kidney diseases and also in those with diabetic nephropathy., „Murine double minute 2“ (Mdm2) ist eine E3-Ubiquitin-Ligase, die das Zellwachstum via Inhibition des Tumorsupressorproteins p53 fördert. Die Blockade dieses Enzyms durch das Kleinmolekül Nutlin-3a wird derzeit wegen seines potentiellen Nutzens in der Krebstherapie in klinischen Studien getestet. Die möglichen Nebenwirkungen von Nutlin-3a in gesunden Geweben, bedingt durch die Störung der Zellhomöostase auf Grund Konzentrationsverschiebungen zwischen p53 und Mdm2, geben jedoch Anlass zur Sorge. In einem acute-kidney-injury(AKI)-Mausmodell zeigte die Verabreichung von Nutlin-3a eine verminderte Heilungsfähigkeit. Zudem zeigte die spezifische Mdm2-Deletion in Podozyten und Tubuluszellen eine signifikante Beeinträchtigung der Nierenfunktion, einhergehend mit der Einleitung von Podoptosis (p53-overexpression dependent cell death). Auf Grund dieser Beobachtungen stellten wir die Hypothese auf, dass die Gabe von Nutlin-3a in gesunden Mäusen die Nierenfunktion durch Podoptosis der Podozyten und Tubuluszellen schädigt. Im Einklang mit der Hypothese beobachteten wir durch die Stimulation von Mauspodozyten- und Maustubuluszell-Kulturen mit Nutlin-3a vermehrten Zelluntergang. Zudem verursachte die Nutlin-3a-Verabreichung in gesunden Mäusen die Stabilisierung von p53 mit resultierender Funktionsbeeinträchtigung der glomerulären Filtrationsbarriere und Albuminurie aufgrund einer Podocytopenie. Es konnte weiterhin eine vermehrte Makrophageninfiltration, eine Hochregulation von Markern der Tubulusschädigung und Entzündungsreaktion, sowie erhöhtes Blut-Harnstoff-Stickstoff beobachtet werden. Bei der Planung einer Nutlin-3a-Therapie, muss deshalb eine potentielle Nierenschädigung nach Blockade von Mdm2 Berücksichtigung finden. Da sich eine Mdm2-Blockade in chronischen Glomerulopathien durch die Inhibition der mitotischen Katastrophe auch positiv auswirken kann, stellten wir die Hypothse auf, dass Nutlin-3a die diabetischen Nephropathie verbessern kann, indem Entzündungsreaktion und die mitotische Katastrophe in Podozyten unterdrückt werden. Erwartungsgemäß zeigte sich nach Nutlin-3a Gabe in diabetischen Mäusen reduzierte Inflammation und Fibrose, aber die Schädigung von Podozyten war nicht vermindert und die Nierenfunktion dadurch nicht verbessert. Entgegen der ursprünglichen Annahme, wurde im Vergleich zu Plazebo eine schlechtere Nierenfunktion hinsichtlich Blut-Harnstoff-Stickstoff, als auch eine signifikantere Podozytopenie beobachtet. Diese unerwarteten Ergebnisse unterstützen jedoch eine neuere Arbeit in metabolomics und computational network analysis von Saito et al., in welcher Mdm2 als ein wichtiges heruntergeregeltes Protein bei diabetischer Nierenerkrankung aufgezeigt wurde. Zusammenfassend kann die therapeutische Mdm2-Blockade eine Schädigung der Nierenfunktion sowohl in Nierengesunden, als auch in Patienten mit diabetischen Nephropathien begünstigen.

Twelve autosomal and 8 X chromosome Alu markers were genotyped for the first time in 161 Central and West Yakuts to test their ability to reconstruct the genetic history of these populations, the northernmost Turkic-speaker ethnic group living in Siberia. Autosomal data revealed that both groups showed extremely close genetic distances to other populations of Siberian origins that occupied areas from Lake Baikal, the ancestral place of origin of Yakuts, to North Siberia, their current territories. Autosomal and X chromosome data revealed some discrepancies on the genetic differentiation and the effective sizes of Central and West Yakuts. Such discrepancies could be related to the patrilineal and occasionally polygamous structure of these populations. Autosomal and X Alu markers are informative markers to reconstruct population past demography and history, but their utility is limited by the available data. This study represents a contribution for further investigations on these populations. © 2013 E. Schweizerbart'sche Verlagsbuchhandlung, Stuttgart, Germany.