Reversing immunosuppression in the tumor microenvironment of fibrolamellar carcinoma via PD-1 and IL-10 blockade.

Fibrolamellar carcinoma (FLC) is a rare liver tumor driven by the DNAJ-PKAc fusion protein that affects healthy young patients. Little is known about the immune response to FLC, limiting rational design of immunotherapy. Multiplex immunohistochemistry and gene expression profiling were performed to characterize the FLC tumor immune microenvironment and adjacent non-tumor liver (NTL). Flow cytometry and T cell receptor (TCR) sequencing were performed to determine the phenotype of tumor-infiltrating immune cells and the extent of T cell clonal expansion. Fresh human FLC tumor slice cultures (TSCs) were treated with antibodies blocking programmed cell death protein-1 (PD-1) and interleukin-10 (IL-10), with results measured by cleaved caspase-3 immunohistochemistry. Immune cells were concentrated in fibrous stromal bands, rather than in the carcinoma cell compartment. In FLC, T cells demonstrated decreased activation and regulatory T cells in FLC had more frequent expression of PD-1 and CTLA-4 than in NTL. Furthermore, T cells had relatively low levels of clonal expansion despite high TCR conservation across individuals. Combination PD-1 and IL-10 blockade signficantly increased cell death in human FLC TSCs. Immunosuppresion in the FLC tumor microenvironment is characterized by T cell exclusion and exhaustion, which may be reversible with combination immunotherapy.

Hypoxia as a barrier to immunotherapy in pancreatic adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDA) is a lethal disease with limited response to cytotoxic chemoradiotherapy, as well as newer immunotherapies. The PDA tumor microenvironment contains infiltrating immune cells including cytotoxic T cells; however, there is an overall immunosuppressive milieu. Hypoxia is a known element of the solid tumor microenvironment and may promote tumor survival. Through various mechanisms including, but not limited to, those mediated by HIF-1α, hypoxia also leads to increased tumor proliferation and metabolic changes. Furthermore, epithelial to mesenchymal transition is promoted through several pathways, including NOTCH and c-MET, regulated by hypoxia. Hypoxia-promoted changes also contribute to the immunosuppressive phenotype seen in many different cell types within the microenvironment and thereby may inhibit an effective immune system response to PDA. Pancreatic stellate cells (PSCs) and myofibroblasts appear to contribute to the recruitment of myeloid derived suppressor cells (MDSCs) and B cells in PDA via cytokines increased due to hypoxia. PSCs also increase collagen secretion in response to HIF-1α, which promotes a fibrotic stroma that alters T cell homing and migration. In hypoxic environments, B cells contribute to cytotoxic T cell exhaustion and produce chemokines to attract more immunosuppressive regulatory T cells. MDSCs inhibit T cell metabolism by hoarding key amino acids, modulate T cell homing by cleaving L-selectin, and prevent T cell activation by increasing PD-L1 expression. Immunosuppressive M2 phenotype macrophages promote T cell anergy via increased nitric oxide (NO) and decreased arginine in hypoxia. Increased numbers of regulatory T cells are seen in hypoxia which prevent effector T cell activation through cytokine production and increased CTLA-4. Effective immunotherapy for pancreatic adenocarcinoma and other solid tumors will need to help counteract the immunosuppressive nature of hypoxia-induced changes in the tumor microenvironment. Promising studies will look at combination therapies involving checkpoint inhibitors, chemokine inhibitors, and possible targeting of hypoxia. While no model is perfect, assuring that models incorporate the effects of hypoxia on cancer cells, stromal cells, and effector immune cells will be crucial in developing successful therapies.

The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies.

BACKGROUND: Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes. METHODS: We used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome. We combined four Illumina large insert size mate paired libraries with 52x of Pacific Biosciences long reads to correct misassembled regions and reduced the number of scaffolds. We then used genotyping by sequencing (GBS) methods to increase the proportion of the assembly anchored to chromosomes. RESULTS: The scaffold number decreased from 4,792 in assembly V1 to 554 in V2 while the scaffold N50 size has increased from 0.47 Mb in V1 to 6.5 Mb in V2. A total of 96.7% of the assembly was anchored to the 10 chromosomes compared to 66.8% in the previous version. Unknown sites (Ns) were reduced from 10.8% to 5.7%. In addition, we updated the functional annotations and performed a new RefSeq structural annotation based on RNAseq evidence. CONCLUSION: Theobroma cacao Criollo genome version 2 will be a valuable resource for the investigation of complex traits at the genomic level and for future comparative genomics and genetics studies in cacao tree. New functional tools and annotations are available on the Cocoa Genome Hub ( http://cocoa-genome-hub.southgreen.fr ).

Construction and characterization of a BAC library for functional genomics in Xenopus tropicalis.

Large insert genomic DNA libraries are useful resources for genomic studies. Although the genome of Xenopus tropicalis stands as the amphibian reference genome because it benefitted from large-scale sequencing studies, physical mapping resources such as BAC libraries are lagging behind. Here we present the construction and characterization of a BAC library that covers the whole X. tropicalis genome. We prepared this BAC library from the genomic DNA of X. tropicalis females of the Adiopodoume strain. We characterized BAC clones by screening for specific loci, by chromosomal localization using FISH and by systematic BAC end sequencing. The median insert size is about 110kbp and the library coverage is around six genome equivalents. We obtained a total of 163,787 BAC end sequences with mate pairs for 77,711 BAC clones. We mapped all BAC end sequences to the reference X. tropicalis genome assembly to enable the identification of BAC clones covering specific loci. Overall, this BAC library resource complements the knowledge of the X. tropicalis genome and should further promote its use as a reference genome for developmental biology studies and amphibian comparative genomics.

Application of thrombin based fibrin glue and non-thrombin based batroxobin glue on intact human blood vessels: evidence for transmural thrombin activity.

An alternative method of uniting small diameter vessels to obtain tissue union while limiting the thrombogenic effect of suture placement at a vessel anastomosis involves the use of a thrombin based fibrin glue as a surgical sealant. This investigation addresses whether the in vitro application of a thrombin based glue (TG), or batroxobin glue (BG), a non-thrombin based glue made with the snake venom enzyme batroxobin, alters intravascular platelet deposition (PD) or cleaves blood fibrinogen, as measured by fibrinopeptide A (FPA) production, when the respective glue is applied to the external surface of an intact human placental artery or an artery with an anastomosis. When TG was applied to the adventitial surface of an intact vessel or an anastomosis (n = 7) of control and experimental vessels, there was a significant increase in intraluminal platelet deposition, an effect not realized with BG (n = 12, intact vessel TG p = 0.01, BG p = 0.66, anastomosis TG p <0.01, BG p <0.01). Both TG and BG significantly increased FPA levels when human whole blood was perfused through both intact vessels or vessels containing an anastomosis when compared to control vessels (intact vessel TG and BG p <0.01, anastomosis TG and BG p <0.01). Labelled thrombin studies document the rapid passage of thrombin through an intact vessel wall or vessels with an anastomosis when TG was applied to the adventitial surface of the vessel. The data suggest that TG and BG are drug delivery systems for their respective enzymes that either pass through or transfer a message across not only a surgically created anastomosis, but also an intact vessel wall.

Thrombin activity on dissected and anastomosed human arteries.

The mechanism of anastomotic thrombosis in microvascular surgery remains poorly understood. We hypothesized that thrombin activity at anastomoses plays a major role in this process. To study this, a surgically relevant human artery anastomosis model was used to (i) measure surface thrombin activity on anastomoses and on intact vessel, (ii) determine the inhibitability of surface thrombin by heparin and recombinant hirudin (r-hirudin), and (iii) determine the anastomotic and intact vessel binding capacity for additional thrombin. Human placental artery segments were placed in chambers in which 0.2 cm2 of luminal surface was exposed to citrated platelet-poor plasma for 10 min at 37 degrees C. The fibrinopeptide A (FPA) concentration (indicating the action of thrombin on fibrinogen) in the supernatant was then measured using an ELISA assay. Intact vessels and anastomoses expressed equivalent thrombin activity that could not be inhibited by heparin at a concentration (0.3 U/ml) that is sufficient to prolong the activated partial thromboplastin time two-fold. Conversely, the concentration of heparin routinely used in intraoperative vessel irrigation solutions (50 U/ml) was able to completely block thrombin activity at both sites. r-Hirudin (0.3 heparin equivalent anti-IIa U/ml) was able to inhibit nearly all of the thrombin activity on each site. Each site was able to bind and express the activity of additional thrombin, indicating the potential for increased vessel thrombogenicity after local clot has formed and has been removed. These data indicate the presence of thrombin on dissected human vessels and its presence in equal amounts on intact and anastomosed vessels when measurement is made before blood flow resumes. Furthermore, vessel-associated thrombin is resistant to a standard systemic concentration of heparin but is susceptible to the much higher heparin concentration that can be delivered locally by the surgeon during vessel irrigation.

Tissue factor and its inhibition at the human microvascular anastomosis.

The surgically created vascular anastomosis is a thrombogenic zone of uncertain etiology. This study was designed to investigate the importance of tissue factor as a cause of human microvascular thrombogenicity. The ability of tissue factor pathway inhibitor (TFPI) to block the effect of tissue factor was also tested in this whole-vessel model system. Tissue factor activity in the presence of absence of TFPI was assayed on the luminal surface of dissected human placental arteries, on the advential surface, and also at the site of a microvascular anastomosis. Vessel wall thrombin activity was measured in the presence and absence of TFPI. Platelet deposition onto a vessel surface using a perfusion system was measured with and without TFPI. Tissue factor activity was greater on the adventitia (4.6 +/- 2.8 x 10(-4) units factor Xa generated/min) than on the endothelium (1.8 +/- 1.6 x 10(-4), P < 0.03) or at a surgically created anastomosis (2.1 +/- 1.2 x 10(-4), P < 0.04). TFPI reduced Xa generation to undetectable levels in 21 of 23 endothelial, adventitial, and anastomotic segments (P < 0.002). TFPI significantly reduced vessel wall thrombin activity in comparison to control anastomoses (control, 3.2 +/- 1.7 ng fibrinopeptide A (FPA)/(ml x min); TFPI, 1.4 +/- 1.2 ng FPA/(ml x min); P < 0.0001). TFPI reduced the platelet deposition on vessel segments with intact endothelium (no TFPI, 0.88 +/- 0.69 x 10(6) platelets/cm2; TFPI, 0.49 +/- 0.29 x 10(6) platelets/cm2; P < 0.06) and on vessel segments with anastomoses (no TFPI, 1.3 +/- 0.70 x 10(6) platelets/cm2; TFPI, 0.76 +/- 0.35 x 10(6) platelets/cm2; P < 0.02). This study demonstrates the importance of tissue factor as a thrombogenic element in a human whole-vessel model system. TFPI is effective in reducing this thrombogenicity.

A new photopolymerizable blood vessel glue that seals human vessel anastomoses without augmenting thrombogenicity.

A new nonbiologic photopolymerizable glue, polyethyleneglycol 400 diacrylate, was studied with respect to its mechanical and biochemical interaction with human blood vessels. Using the human placental artery model, we tested the ability of polyethyleneglycol 400 diacrylate to prevent leakage of blood at the site of vascular anastomoses, which are made porous by the presence of tissue gaps and suture puncture sites. Fibrin glue is known to augment local vessel thrombogenicity through the presence of the coagulation enzyme thrombin. We tested the effect of externally applied polyethyleneglycol 400 diacrylate (which does not contain thrombin) on luminal thrombin activity and platelet deposition from flowing human blood. At a shear rate of 312 per second and a transmural pressure of 80 cm H2O, the leakage rate of saline from human placental artery anastomoses was 1.0 +/- 1.2 ml/min (n = 8). When the same anastomoses were then glued, 7 of 8 of the anastomoses leaked less than 0.05 ml/min (p < 0.05). Platelet deposition to human vessels was not influenced by the external application of polyethyleneglycol 400 diacrylate either on intact vessels (no polyethyleneglycol 400 diacrylate, 0.51 +/- 0.28 x 10(6) platelets/cm2; with polyethyleneglycol 400 diacrylate, 0.47 +/- 0.26 x 10(6) platelets/cm2; n = 7) or at anastomoses (no polyethyleneglycol 400 diacrylate, 0.69 +/- 0.36 x 10(6) platelets/cm2; with polyethyleneglycol 400 diacrylate, 0.53 +/- 0.33 x 10(6) platelets/cm2; n = 8), p > 0.05.(ABSTRACT TRUNCATED AT 250 WORDS)