CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data.

BACKGROUND: With the increase of the dimensionality in flow cytometry data over the past years, there is a growing need to replace or complement traditional manual analysis (i.e. iterative 2D gating) with automated data analysis pipelines. A crucial part of these pipelines consists of pre-processing and applying quality control filtering to the raw data, in order to use high quality events in the downstream analyses. This part can in turn be split into a number of elementary steps: signal compensation or unmixing, scale transformation, debris, doublets and dead cells removal, batch effect correction, etc. However, assembling and assessing the pre-processing part can be challenging for a number of reasons. First, each of the involved elementary steps can be implemented using various methods and R packages. Second, the order of the steps can have an impact on the downstream analysis results. Finally, each method typically comes with its specific, non standardized diagnostic and visualizations, making objective comparison difficult for the end user. RESULTS: Here, we present CytoPipeline and CytoPipelineGUI, two R packages to build, compare and assess pre-processing pipelines for flow cytometry data. To exemplify these new tools, we present the steps involved in designing a pre-processing pipeline on a real life dataset and demonstrate different visual assessment use cases. We also set up a benchmarking comparing two pre-processing pipelines differing by their quality control methods, and show how the package visualization utilities can provide crucial user insight into the obtained benchmark metrics. CONCLUSION: CytoPipeline and CytoPipelineGUI are two Bioconductor R packages that help building, visualizing and assessing pre-processing pipelines for flow cytometry data. They increase productivity during pipeline development and testing, and complement benchmarking tools, by providing user intuitive insight into benchmarking results.

The thermostability of the RTS,S/AS01 malaria vaccine can be increased by co-lyophilizing RTS,S and AS01.

BACKGROUND: Developing thermostable vaccines is a challenge for pharmaceutical companies due to the inherent instability of biological molecules in aqueous solution. The problem is even more stringent in regions subjected to high temperatures in which protective cold chain is difficult to maintain due to a lack of infrastructure. Here, a simple, cost-effective solution to increase the thermostability of the malaria candidate vaccine RTS,S/AS01 is described. This vaccine currently needs to be stored between 2 and 8  °C due to the sensitivity of liquid AS01 to higher temperatures. The strategy was to increase thermostability by co-lyophilizing the RTS,S antigen and AS01. METHODS: Co-lyophilization was achieved in a solution containing 5% sucrose, 10 mM potassium phosphate and 0.0312% polysorbate 80 at pH 6.1. The physicho-chemical characteristics and immunogenic properties of the resulting solid product, called CL-vac, fresh or stored at high temperature, were compared to those of the candidate RTS,S/AS01. RESULTS: CL-vac proved to be acceptable in terms of visual appearance and physico-chemical characteristics. The structural integrity of both RTS,S and AS01 within CL-vac and its equivalence to the RTS,S/AS01 candidate vaccine were shown. Further, the stability of CL-vac was demonstrated for storage periods including 1 year at 4  °C, 1 year at 30  °C, and up to 6 months at 37  °C. In addition, CL-vac could withstand a heat excursion consisting of 1 month at 45  °C after storage for 1 year at 30  °C. Equivalence and stability were demonstrated by the various analytical tools and the immunogenicity of the samples after storage was also demonstrated in mice. CONCLUSIONS: In conclusion, the co-lyophilization process appeared as a promising approach to increase RTS/AS01 vaccine thermostability.

Comprehensive Characterization of Reference Standard Lots of HIV-1 Subtype C Gp120 Proteins for Clinical Trials in Southern African Regions.

Two HIV-1 subtype C gp120 protein candidates were the selected antigens for several experimental vaccine regimens now under evaluation in HVTN 100 Phase I/II clinical trial aiming to support the start of the HVTN 702 Phase IIb/III trial in southern Africa, which is designed to confirm and extend the partial protection seen against HIV-1 infection in the RV144 Thai trial. Here, we report the comprehensive physicochemical characterization of the gp120 reference materials that are representative of the clinical trial materials. Gp120 proteins were stably expressed in Chinese Hamster Ovary (CHO) cells and subsequently purified and formulated. A panel of analytical techniques was used to characterize the physicochemical properties of the two protein molecules. When formulated in the AS01 Adjuvant System, the bivalent subtype C gp120 antigens elicited 1086.C- and TV1.C-specific binding antibody and CD4+ T cell responses in mice. All the characteristics were highly representative of the Clinical Trial Materials (CTM). Data from this report demonstrate the immunogenicity of the gp120 antigens, provide comprehensive characterization of the molecules, set the benchmark for assessment of current and future CTM lots, and lay the physicochemical groundwork for interpretation of future clinical trial data.

Heterologous prime-boost regimens with a recombinant chimpanzee adenoviral vector and adjuvanted F4 protein elicit polyfunctional HIV-1-specific T-Cell responses in macaques.

HIV-1-specific CD4+ and CD8+ T lymphocytes are important for HIV-1 replication control. F4/AS01 consists of F4 recombinant fusion protein (containing clade B Gag/p24, Pol/RT, Nef and Gag/p17) formulated in AS01 Adjuvant System, and was shown to induce F4-specific polyfunctional CD4+ T-cell responses in humans. While replication-incompetent recombinant HIV-1/SIV antigen-expressing human adenoviral vectors can elicit high-frequency antigen-specific CD8+ T-cell responses, their use is hampered by widespread pre-existing immunity to human serotypes. Non-human adenovirus serotypes associated with lower prevalence may offer an alternative strategy. We evaluated the immunogenicity of AdC7-GRN ('A'), a recombinant chimpanzee adenovirus type 7 vector expressing clade B Gag, RT and Nef, and F4/AS01 ('P'), when delivered intramuscularly in homologous (PP or AA) and heterologous (AAPP or PPAA) prime-boost regimens, in macaques and mice. Vaccine-induced HIV-1-antigen-specific T cells in peripheral blood (macaques), liver, spleen, and intestinal and genital mucosa (mice) were characterized by intracellular cytokine staining. Vaccine-specific IgG antibodies (macaques) were detected using ELISA. In macaques, only the heterologous prime-boost regimens induced polyfunctional, persistent and balanced CD4+ and CD8+ T-cell responses specific to each HIV-1 vaccine antigen. AdC7-GRN priming increased the polyfunctionality of F4/AS01-induced CD4+ T cells. Approximately 50% of AdC7-GRN-induced memory CD8+ T cells exhibited an effector-memory phenotype. HIV-1-specific antibodies were detected with each regimen. In mice, antigen-specific CD4+ and CD8+ T-cell responses were detected in the mucosal and systemic anatomical compartments assessed. When administered in heterologous prime-boost regimens, AdC7-GRN and F4/AS01 candidate vaccines acted complementarily in inducing potent and persistent peripheral blood HIV-1-specific CD4+ and CD8+ T-cell responses and antibodies in macaques. Besides, adenoviral vector priming modulated the cytokine-expression profile of the protein-induced CD4+ T cells. Each regimen induced HIV-1-specific T-cell responses in systemic/local tissues in mice. This suggests that prime-boost regimens combining adjuvanted protein and low-seroprevalent chimpanzee adenoviral vectors represent an attractive vaccination strategy for clinical evaluation.

Comparison of the immune responses induced by soluble and particulate Plasmodium vivax circumsporozoite vaccine candidates formulated in AS01 in rhesus macaques.

We have designed a pre-erythrocytic vaccine candidate based on the Plasmodium vivax circumsporozoite (CSV) protein, which includes its N- and C-terminal parts and a truncated region containing repeat sequences from both the VK210 and the VK247 P. vivax subtypes. Two versions of this vaccine candidate were made: a soluble recombinant protein expressed in Escherichia coli, designated VMP001 and a particulate antigen expressed in Saccharomyces cerevisiae, designated CSV-S,S. The latter is composed of CSV-S, a fusion protein between VMP001 and hepatitis B surface antigen (HBsAg), and free HBsAg co-expressed in yeast and self-assembling into mixed particles. Both antigen versions, adjuvanted with AS01, were shown to be immunogenic in rhesus monkeys. CSV-S,S/AS01 induced higher levels of VMP001-specific antibodies than did VMP001/AS01. Antibody responses against the N- and C-terminal regions of CSV and the VK210 repeat motif were of a similar magnitude following immunization with either the soluble or the particulate antigen. However, antibodies against the AGDR region, a potentially protective B cell epitope, were only detected after immunization with CSV-S,S. Analysis of the induced CD4(+) T cells highlighted different cytokine profiles depending on the antigen form. These results warrant further clinical evaluation of these two vaccine candidates to assess the added value of a particulate versus soluble form of CSV, in terms of both immunogenicity and protective efficacy.

Improved T cell responses to Plasmodium falciparum circumsporozoite protein in mice and monkeys induced by a novel formulation of RTS,S vaccine antigen.

Protection against Plasmodium falciparum sporozoite infection can be achieved by vaccination with the recombinant circumsporozoite protein-based vaccine RTS,S formulated with the AS02A Adjuvant System. Since this protection is only partial and wanes over time, we have developed a new RTS,S-based vaccine adjuvanted with AS01B. RTS,S/AS01B-induced high specific antibody titers and increased the frequency of mouse CD4(+) and CD8(+) T cells expressing IFN-gamma, and of monkey CD4(+) T cells expressing IL-2 and/or IFN-gamma and/or TNF-alpha upon stimulation with vaccine antigens. Our data provides clear evidence that combining RTS,S antigen with a potent adjuvant induces strong humoral and cellular responses in vivo.

Priming with an adenovirus 35-circumsporozoite protein (CS) vaccine followed by RTS,S/AS01B boosting significantly improves immunogenicity to Plasmodium falciparum CS compared to that with either malaria vaccine alone.

The RTS,S/AS02A protein-based vaccine consistently demonstrates significant protection against infection with Plasmodium falciparum malaria and also against clinical malaria and severe disease in children in areas of endemicity. Here we demonstrate with rhesus macaques that priming with a replication-defective human adenovirus serotype 35 (Ad35) vector encoding circumsporozoite protein (CS) (Ad35.CS), followed by boosting with RTS,S in an improved MPL- and QS21-based adjuvant formulation, AS01B, maintains antibody responses and dramatically increases levels of T cells producing gamma interferon and other Th1 cytokines in response to CS peptides. The increased T-cell responses induced by the combination of Ad35.CS and RTS,S/AS01B are sustained for at least 6 months postvaccination and may translate to improved and more durable protection against P. falciparum infection in humans.

Analysis of serum prostate-specific antigen levels in men aged 40 years and older in Yasuj, Iran.

INTRODUCTION: Serum prostate-specific antigen (PSA) is still the simplest marker for early diagnosis and follow-up of prostate cancer. Because racial differences in PSA levels have been found, we performed this study to determine the reference level of serum PSA for men in Yasuj, in southwest Iran. MATERIALS AND METHODS: Men aged 40 years and older who had been referred to any of the Yasuj hospitals for a blood cell count for any reason were randomly selected. Those with a history of prostate cancer, prostatitis, urinary tract infection, bladder outlet obstruction, or transurethral procedures were excluded. Blood samples were taken, and PSA levels were measured. RESULTS: Prostate-specific antigen levels in the 95th percentile were 1.35 ng/mL, 1.85 ng/mL, 3.2 ng/mL, and 4.4 ng/mL for men aged 40 to 49, 50 to 59, 60 to 69, and older than 69 years, respectively. Mean serum PSA levels were 0.7 ng/mL, 0.9 ng/mL, 1.6 ng/mL, and 2.2 ng/mL, respectively. CONCLUSION: A comparison of our results with those from studies in the United States and Japan shows that the reference PSA level in our society is significantly lower than that for white and black Western men, and slightly lower than that for Japanese men. Although we examined men with no history of prostate cancer, cancer was not ruled out by diagnostic test; hence, our results may be overestimated. Further investigations in Iran are warranted.