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In this study we investigated the transcriptome and epigenome dynamics of the tomato fruit during post-harvest in a landrace belonging to a group of tomatoes (Solanum lycopersicum L.) collectively known as “Piennolo del Vesuvio”, all characterized by a long shelf-life. Expression of protein-coding genes and microRNAs as well as DNA methylation patterns and histone modifications were analysed in distinct post-harvest phases. Multi-omics data integration contributed to the elucidation of the molecular mechanisms underlying processes leading to long shelf-life. We unveiled global changes in transcriptome and epigenome. DNA methylation increased and the repressive histone mark H3K27me3 was lost as the fruit progressed from red ripe to 150 days post-harvest. Thousands of genes were differentially expressed, about half of which were potentially epi-regulated as they were engaged in at least one epi-mark change in addition to being microRNA targets in ~5% of cases. Down-regulation of the ripening regulator MADS-RIN and of genes involved in ethylene response and cell wall degradation was consistent with the delayed fruit softening. Large-scale epigenome reprogramming that occurred in the fruit during post-harvest likely contributed to delayed fruit senescence.

Background: Myelodysplastic syndromes (MDS) have been associated with alterations in the bone marrow microenvironment and include abnormal innate and adaptive immune responses. The extent to which these changes contribute to the pathogenesis of MDS is unclear. The heterogeneous nature of MDS makes it difficult to distinguish changes in intrinsic cell function for microenvironmental alterations in the mutated myeloid compartment. T cells, which are in the lymphoid compartment and less frequently contain MDS mutations, can potentially be used to evaluate immune dysfunction in the presence of malignant myeloid cells. Here we examine the immunophenotypes and proliferative function of T lymphocyte and monocyte populations from higher-risk MDS patients. Methods: Peripheral blood mononuclear cells (PBMC) from patients with IPSS-R Intermediate/High/Very High-risk MDS (herein referred to collectively as higher-risk MDS) and age-matched healthy donors (n = 15 and n = 12, respectively) were polyclonally stimulated with an antibody against CD3 (OKT3) in the presence of IL-2 (50 U/mL). Phenotypic analysis was performed at baseline and 46 hours after the addition of OKT3 and IL-2. T cell proliferation was measured by staining PBMC with proliferation dye (CellTrace Violet) and measuring fold proliferation after eight days in culture. Proliferation statistical comparisons were made by unpaired t-test. Phenotypic parameters were measured by flow cytometry and statistical analysis performed with the Kruskal-Wallis one-way analysis. Results: As previously reported, higher-risk MDS patient T cells had decreased capacity for proliferation when compared to healthy donor counterparts (Figure 1A p = 0.0096). This difference in proliferative capacity was not associated with either the level of PD-1 on the surface of T cells (r = 0.2956) or the level of PD-L1 on monocytes (r = 0.3859) in stimulated PBMCs. Patients with higher-risk MDS tended to have lower PD-L1 surface expression on monocytes compared to healthy donor counterparts, albeit not significantly (Figure 1C p = 0.1). However, PD-1 expression on T cells was comparable between groups both before and after stimulation (Figure 1B CD4 cells: p = 0.58; CD8 cells p = 0.58). This suggests that T cell proliferation from patients with higher-risk MDS might not be inhibited through the PD-1/PD-L1 axis. Of note, higher-risk MDS patient monocytes expressed less CD80 and HLA-DR both pre- and post-stimulation when compared to healthy donors (Figure 1C CD80: p = 0.0001 and 0.037; DR: p = 0.012 and 0.019, respectively), implying a potential dysfunction in the monocytic stimulatory and antigen presentation capacity. PD-L1 surface expression is low at baseline (an average of Conclusion: There was no significant difference in PD-1 and PD-L1 expression between higher-risk MDS and healthy donor patients, despite reduced T cell proliferation among patients with MDS. Additionally, decreased levels of CD80 and HLA-DR on intermediate/high-risk MDS patient monocytes suggests a suppressed ability to upregulate activation markers, possibly leading to decreased T cell proliferation. Targeting the PD-1/PD-L1 axis alone may not be therapeutic in patients with higher-risk MDS, and we hypothesize that the immune evasion observed in higher-risk MDS patients may not be due exclusively to increases in inhibitory interactions like PD-L1 and PD-1, but may result from a decrease in stimulatory receptors, such as CD80, and antigen presentation molecules, such as HLA-DR. Disclosures Fields: PersImmune, Inc.: Ended employment in the past 24 months. Ferrari:PersImmune, Inc.: Ended employment in the past 24 months. Tarke:PersImmune, Inc.: Ended employment in the past 24 months. Luger:Arcturus Therapeutics: Current Employment. Lane:PersImmune, Inc.: Current Employment. Vitiello:PersImmune, Inc.: Current equity holder in private company, Ended employment in the past 24 months. Bejar:Aptose Biosciences, Inc: Current Employment, Current equity holder in publicly-traded company.

Background: Myelodysplastic Syndromes (MDS) are a heterogeneous hematologic malignancy characterized by bone marrow failure and cytopenias. The median survival rate for patients with higher-risk MDS who fail standard-of-care chemotherapy with hypomethylating agents (HMAs) is less than 6 months, and the only curative treatment for these patients is hematopoietic stem cell transplant (HSCT). Over the past 10 years, immunotherapy as a cancer treatment has achieved variable levels of success in different tumor types. There are currently 22 active clinical trials of immunotherapies for MDS (www.clinicaltrials.gov; 7/30/19), including our phase I clinical trial with a personalized adoptive cellular therapy targeting MDS patient neoantigens (NCT 03258359). Because MDS patients are frequently monocytopenic and the existing literature is inconsistent regarding the ability of MDS patients' monocytes to support T cell activation, we compared the activation of MDS T cells with those of healthy donors in the presence of autologous monocytes. Methods: Peripheral blood mononuclear cells (PBMC) from 5 healthy donors and 7 higher-risk MDS patients were cryopreserved after Ficoll separation. These PBMC were thawed and aliquoted into 6 replicate wells of 200,000 cells in 96-well u-bottom plates in R-10 culture medium. Half of the wells were treated with 25 ng/mL OKT3 and 200 U/mL IL-2. After 48 hours at 37˚C with 5% CO2, the wells were collected for analysis by flow cytometry. Beads were used to detect T cell activation induced secretion of IFNg, TNFa, IL-4, IL-10, and IL-17 in the supernatant and fluorescent antibodies were used to phenotype viable cells for CD3, CD4, CD8, and the T cell activation markers, CD69, CD25, CTLA-4, PD-1, and HLA-DR. Results: We measured a higher release of IFNg and TNFa in donor PBMC compared to MDS patients after OKT3/IL-2 activation, p < 0.01 and 0.04, respectively by 2-way ANOVA. The expression of CD69, CD25, HLA-DR, and CTLA4 increased variably on activated T cells from donors or MDS patients, but expression of CD4+CD25+ was more frequent on donor T cells after activation (p = 0.03). Activation also resulted in a higher frequency of PD-1 expression on donor CD4+ and CD8+ T cells than on MDS T cells (p < 0.01 and < 0.01, respectively). Interestingly, on both MDS and normal T cells the percentage of CD8+PD1+ activated cells correlated strongly with the percent of CD14+ monocytes present in the PBMC (R2 = 0.92 and 0.60 respectively; Fig 1a and 1b). We designed further experiments to test whether this was a patient intrinsic phenomenon, or if the absolute number of CD14+ monocytes in the PBMC was associated with different levels of PD1 expression upon T cell activation. First, we separated CD14+ cells from the PBMC of a patient with MDS using magnetic beads. Then CD14+ cells were added back to the CD14-depleted PBMC at a final percent of 0.5, 5, 10, 20, 35, 70, or 100% of the original amount. Unmodified PBMC was included as a control and all cells were stimulated with OKT3 and IL-2 or left in R-10 medium without stimulus. After 24, 48, and 70 hours, samples were collected to analyze by flow cytometry for CD3, CD4, CD8, CD14, and PD1 expression. The results show that an increasing percent of monocytes corresponded to the increased expression of PD1 on CD8+ and CD4+ T cells. Conclusion: Our results show that there are variable reductions in markers of T cell activation and cytokine secretion in MDS patients compared to healthy donors. We also observed that the fold increase in activation induced PD-1 expression was well correlated with the percent of CD14+ monocytes in the PBMC of both MDS patients and healthy donors. Direct experimentation revealed that this correlation is a cause-effect relationship. We are continuing to investigate the role of monocytes in T cell activation in MDS patients. Disclosures Bejar: Celgene: Consultancy; Takeda Pharmaceuticals: Research Funding; AbbVie/Genentech: Consultancy, Honoraria; Astex/Otsuka: Consultancy; Modus Outcomes: Consultancy; Daiichi-Sankyo: Consultancy. Lane:PersImmune, Inc.: Employment.

Background: There are few therapeutic options for higher risk patients with myelodysplastic syndrome (MDS) who fail standard therapy, and their 2-year survival rate is approximately 15%. Here we report on a recently initiated collaborative (industry-academia) first-in-human phase 1 clinical trial to assess the safety and tolerability of a novel form of adoptive T cell immunotherapy for such patients that targets patient and disease-specific, mutation-derived neoantigens. This experimental therapy is based on the concept that a) cancer is caused by somatic mutations that may generate novel immunogenic proteins (ie, neopeptides and possible neoantigens), b) that the adaptive immune system can be trained ex vivo to recognize neopeptides as neoantigens and c) that infusion of culture-expanded, neoantigen-immunized autologous T cells may be safe and therapeutically effective. Methods: This is an open-label, phase 1, 3+3 dose escalation trial with 3 cell doses (0.3, 1, and 3.0 × 107nucleated cells/kg) in cohorts of 3 patients each (see www.clinicaltrials.gov, NCT-03258359). Eligible subjects are 18 years of age or older and will have Intermediate, High, or Very High risk MDS by the revised International Prognostic Scoring System, with at least one cytopenia, and will have failed or relapsed after 6 cycles of standard hypomethylating therapy or declined such therapy, an ECOG status 0-2, and adequate organ function. Each patient's MDS-related mutations are identified and autologous T cells are immunized ex vivo with peptides corresponding to the mutated protein(s), then expanded and suitability-tested for experimental infusion (referred to as PACTN). Importantly, the T cells must demonstrate neoantigen specificity and must kill autologous MDS stem-progenitor cells prior to qualification for infusion. Each eligible subject receives a single infusion of autologous PACTN followed by intensive monitoring for adverse events (AEs) for 4 weeks and periodic monitoring for 1 year. The primary study end-point (EP) is assessment of dose-limiting toxicity (DLT) and maximum tolerated PACTN dose (MTD). Secondary EPs include disease response 1 month after PACTN infusion, overall and progression-free survival at 6 and 12 months, and assessment of the peak abundance and persistence of the infused T cells in peripheral blood. Exploratory EPs include an assessment of the effect of PACTN infusion on the allele frequencies of the targeted and non-targeted MDS mutations in blood and marrow leukocytes. Results: At this time, two subjects have been infused with PACTN in the first dose cohort. Neither subject had an infusion reaction, severe AE, or DLT after follow-up for 2-3 months, nor has a disease response occurred in these subjects. Of interest, the infused PACTN product in the first subject showed 59% clonal dominance by a single T cell receptor (TCR) clone that was present at only 0.002% in patient's blood prior to T cell immunization with neoantigen related peptides. Multiple additional expanded TCR clones were also identified in the infused PACTN product. The presence of a dominant TCR clone in the PACTN product enabled the assessment of the in vivo abundance and persistence of the clone after PACTN infusion. The dominant clone expanded between day 1 and day+4 after PACTN infusion to a peak frequency of 0.13%, representing a 64-fold expansion of this TCR compared with the pre-infusion sample of blood leukocytes, then decreased to 0.09% by day +8. The clone was also demonstrated in bone marrow on day +15 at a frequency of 0.03%, representing a 20-fold expansion of this TCR clone compared with the pre-infusion marrow sample. Similar studies on the second subject are in progress, and will be continued in future subjects as the clinical trial continues. Finally, our studies show that it has been possible to effectively immunize autologous T cells to patient-specific neoantigens in all patients studied with MDS (n=4) and also all patients with AML (n=3) studied to date. Conclusion: The early results of this clinical trial support the feasibility and safety of this novel approach to adoptive T cell mediated immunotherapy for patients with higher-risk MDS and encourages continuation of the trial in the higher dose level cohorts. Disclosures Ferrari: Persimmune, Inc.: Employment. Tarke:Persimmune, Inc.: Employment. Fields:Persimmune, Inc.: Employment. Ferrari:Persimmune, Inc.: Employment. Ni:Persimmune, Inc.: Employment. Ferrari:Persimmune, Inc.: Employment. Warner:Persimmune, Inc.: Employment. Jochelson:PersImmune, Inc.: Consultancy. Bejar:Celgene: Consultancy, Honoraria; AbbVie/Genentech: Consultancy, Honoraria; Takeda: Research Funding; Genoptix: Consultancy; Modus Outcomes: Consultancy; Foundation Medicine: Consultancy; Astex/Otsuka: Consultancy, Honoraria. Vitiello:Persimmune, Inc.: Employment. Lane:PersImmune, Inc.: Employment.

Cathelicidins (caths) are peptides that are expressed at high levels in neutrophils and some epithelia and can act as natural antibiotics by directly killing a wide range of microorganisms. We hypothesized that caths are expressed in mast cells (MCs), because these cells have been previously associated with inherent antimicrobial activity. Cultured murine MCs contained abundant amounts of cathelin-related antimicrobial peptide (AMP), the murine cath, and this expression was inducible by LPS or lipoteichoic acid. Human skin MCs also expressed cath as detected by immunohistochemical analysis for the human cath LL-37. The functional significance of this expression was shown by comparing MCs cultured from normal mice to MCs from littermates deficient in the cathelin-related AMP gene (Cnlp−). MCs derived from Cnlp−/− animals had a 50% reduction in their ability to kill group A Streptococcus. These MCs expressed equivalent amounts of mRNA for murine β-defensin-4, a β-defensin AMP. Thus, different antimicrobials can be identified in MCs, and the presence of cath is necessary for efficient bacterial killing. These observations suggest that the presence of cath is vital to the ability of mammalian MCs to participate in antimicrobial defense.

Adoptive cellular immunotherapy has proven to be a successful approach in preventing and curing cytomegalovirus infection and Epstein-Barr virus–associated lymphomas after bone marrow transplantation. Translation of this approach for preventing leukemia relapse after bone marrow transplantation might require ex vivo priming and long-term maintenance of leukemia blast-specific T cells. To accomplish this goal, procedures were optimized for the in vitro priming of naive CD8 using dendritic cells activated by CD40 ligation, interleukin-12 (IL-12), and IL-7. Using T lymphocytes and dendritic cells obtained from HLA-matched allogeneic bone marrow transplantation donors and leukemia blasts as a source of tumor antigens, anti–acute myeloid leukemia cytotoxic T lymphocytes (CTLs) were induced. In these experiments, it was found that though it is possible to induce CTLs using immature dendritic cells, IL-12, and IL-7, obtaining long-term CTLs requires the presence of CD4 T cells in the priming phase. Using this approach, long-term antileukemia CTL lines could be generated from 4 of 4 bone marrow donors. Because this procedure does not require definition of the target antigen and because it selects responding cells from a virgin T-cell repertoire, its general application is suggested in adoptive immunotherapy and in the definition of tumor rejection antigens.

A fundamental goal in the study of infections is to understand the dynamic interplay between host and pathogen; however, direct in vivo interrogation of this disease process via transcriptional profiling has been lacking. Here we describe the development and application of novel bacterial RNA amplification technology to simultaneously identify key elements of both host and pathogen responses in a murine infection model. On the bacterial side, we found induction of an unusual pattern of stress response genes, a response to host-induced metal ion limitation, and a failure to achieve stationary phase in vivo. On the mammalian side, we observed the surprising induction of several genes encoding acute phase response proteins including hepcidin, haptoglobin, complement C3 and metallothionein 1 at the site of infection, as well as other mediators of innate immunity. Thus, our results reveal host-pathogen cross-talk not predicted by previous in vitro analyses and provide the framework to eavesdrop on a broad array of host-pathogen interactions in vivo. As described here, the comprehensive examination of host-pathogen interactions during an infection is critical to the discovery of novel approaches for intervention not predicted by current models.

Inhibitor of apoptosis (IAP) family proteins are suppressors of apoptosis that have been implicated in apoptosis resistance in some cancers. Their expression and relevance to the prognosis of prostate cancer were investigated.The expression of four members of the IAP family (cellular inhibitor of apoptosis protein 1, cellular inhibitor of apoptosis protein 2, X chromosome-linked IAP, and survivin) was examined by immunohistochemistry and immunoblotting in human prostate cancers and in prostate tissues from transgenic mice expressing SV40 large T antigen under control of a probasin promoter.Tumor-associated elevations in the levels of all four IAP family members were common in prostate cancers of both humans and mice, suggesting concomitant up-regulation of multiple IAP family proteins. Compared with normal prostatic epithelium, increased IAP expression was often evident even in prostatic intraepithelial neoplasia lesions (carcinoma in situ), suggesting that deregulation of IAP expression occurs early in the pathogenesis of prostate cancer. IAP expression did not correlate with Gleason grade or prostate-specific antigen levels.The findings demonstrate that tumor- associated elevations in the expression of several IAP family proteins occur as a frequent and early event in the etiology of prostate cancer.

Cancer-related mortality can be decreased by prevention, early detection and improved therapies. Although animal models should be used to evaluate the success of cancer therapies, their usefulness is controversial. Many cancer therapies that have cured tumors in mice have not met with similar success when attempted in humans. Current animal models rely mainly on inoculating cell lines into animals, a method that does not reproduce the natural development of the tumor, both for the kinetics of induction and the anatomical site concerned. In this study, we have used an SV40 T-antigen-transgenic mouse model of prostate cancer in which the tumor spontaneously develops orthotopically with a disease progression that closely resembles the progression of human prostate cancer. We have used this model to test the suitability of adoptive cellular immunotherapy. Transfer of naive cells obtained from a T-antigen-negative congenic animal had significant but partial effects: it prevented development of malignant tumors, leaving just minor foci of residual tumor and/or hyperplasia. Adoptive transfer of memory lymphocytes specific for T-antigen, which is a prostatic self antigen in this model, prevented tumor development and progression without affecting the morphology and function of involved tissues. Treated animals were able to breed, and their survival was greatly increased. These results strongly suggest that adoptive immunotherapy should be successful in treating early stages of human prostate cancer.

To study the mechanisms that influence the immunogenicity and immunodominance of potential cytotoxic T lymphocyte (CTL) epitopes, we conducted a systematic analysis of the CTL response raised in HLA-A*0201/Kb (A2/Kb) transgenic mice against the viral antigen, hepatitis B virus polymerase (HBV pol). From a pool of 26 nonamer peptides containing the HLA-A*0201-binding motif, we selected A2-binding peptides, immunized A2/Kb animals, and tested the CTL raised against the peptide for recognition of HBV pol transfectants. Of nine immunogenic CTL epitopes, only four were recognized on HBV pol transfectants, whereas the other five were cryptic. Characterization of the peptide-specific CTL lines indicated that crypticity may result from either poor processing or low T cell receptor (TCR) avidity. To identify the immunodominant epitopes, we determined the CTL specificities induced in A2/Kb animals in response to priming with HBV pol cDNA. We obtained a response against three epitopes that were contained with the set of four epitopes recognized by peptide-specific CTL on HBV pol transfectants. Comparative analysis of cDNA priming and peptide priming revealed, therefore, the presence of a subdominant epitope. We conclude that for the HBV pol antigen, the repertoire of CTL specificities is shaped by major histocompatibility complex class I peptide binding capacity, antigen processing, and TCR availability.

[EN] The long tradition of tomato cultivation in Italy has allowed the evolution of a wide diversity of traditional varieties or landraces that have been cultivated for centuries and many of them are still common in the local markets. Adaptation to peculiar climatic and edaphic conditions, the geographical isolation of several growing areas, the specific agro-technique, the local gardners’ selection, also based on consumers’s sensory preferences, have resulted in groups of landraces distributed not only by region but also by sub-regional areas. In most cases, the cultivation of these Italian landraces covers very limited areas being carried out in family gardens for personal consumption and/or in small-size farms that, therefore, play a key role in the on farm maintenance of this precious germplasm, which in many cases is risking extinction. The Campania region has been, and still is, an important area for tomato production with a long tradition in the selection, cultivation and processing of the crop, resulting in a rich reservoir of valuable tomato landraces. So far, only three Italian tomato landraces have been granted a Protected Geographical Status under European Union law, the PGI “Pomodoro di Pachino” form Sicily, and the two PDOs “Pomodoro S. Marzano dell'Agro Sarnese-Nocerino” and the “Pomodorino del Piennolo del Vesuvio” from Campania. This short review will address some of the most popular landraces of the Campania region, with a particular focus on the two PDOs., [ES] La larga tradición del cultivo del tomate en Italia ha permitido la evolución de una amplia diversidad de variedades tradicionales o variedades autóctonas que han sido cultivadas durante siglos, muchas de las cuales siguen siendo comunes en los mercados locales. La adaptación a las peculiares condiciones climáticas y edáficas, el aislamiento geográfico de varias zonas de cultivo, las técnicas de cultivo específicas, la selección de los agricultores locales, también basada en las preferencias sensoriales de los consumidores, han dado como resultado grupos de variedades locales distribuidas no sólo por regiones, sino por áreas sub-regionales. En la mayoría de los casos, el cultivo de estas variedades autóctonas italianas cubre áreas muy limitadas y se están llevando a cabo en huertos familiares para consumo personal y / o en fincas pequeñas que, por lo tanto, desempeñan un papel clave en el mantenimiento de este valioso germoplasma, que en muchos casos está en peligro de extinción. La región de Campania ha sido, y sigue siendo, un área importante para la producción de tomate con una larga tradición en la selección, cultivo y procesamiento de este cultivo, resultando en un rico reservorio de variedades autóctonas de tomate valiosas. Hasta el momento, sólo tres variedades autóctonas de tomate italiano han obtenido el estatus de protección geográfica conforme a la legislación de la Unión Europea, la IGP “Pomodoro di Pachino” de Sicilia y las dos DOP “Pomodoro S. Marzano dell'Agro Sarnese-Nocerino” y “Pomodorino Del Piennolo del Vesuvio" de Campania. Esta breve revisión abordará algunas de las razas tradicionales más populares de la región de Campania, con especial atención a las dos DOP., This work was supported by the European Commission Horizon 2020 program (TRADITOM grant 634561 to S.G. and P.S.).