Increased carbohydrate production from carbon dioxide in randomly mutated cells of cyanobacterial strain Synechocystis sp. PCC 6714: Bioprocess understanding and evaluation of productivities

Recently, several mutants of Synechocystis sp. PCC 6714 were obtained showing superior PHB content and productivities. Here, the most promising mutant named MT_a24 is compared in detail with the wild-type in controlled photobioreactors. In order to provide an easily scalable and alternative approach to the normally done two-step process -comprising of growth phase and limitation phase- a one-step cultivation was optimized. The multivariate experimental design approach was used for the optimization of the one-step, self-limiting media. During one-step cultivation of MT_a24 with optimized media 30 ± 4% (DCW) corresponding to 1.16 g L^-1 PHB was obtained. Using pulse experiments it was demonstrated that phosphate is the key driver of glycogen synthesis in Synechocystis sp. PCC 6714 and it can be used to boost glycogen productivity. The maximum glycogen content acquired was 2.6 g L^-1 (76.2% DCW) for mutant MT_a24 using phosphate feeding and carbon dioxide as carbon source.

Bioprocess Engineering Aspects of Sustainable Polyhydroxyalkanoate Production in Cyanobacteria

Polyhydroxyalkanoates (PHAs) are a group of biopolymers produced in various microorganisms as carbon and energy reserve when the main nutrient, necessary for growth, is limited. PHAs are attractive substitutes for conventional petrochemical plastics, as they possess similar material properties, along with biocompatibility and complete biodegradability. The use of PHAs is restricted, mainly due to the high production costs associated with the carbon source used for bacterial fermentation. Cyanobacteria can accumulate PHAs under photoautotrophic growth conditions using CO₂ and sunlight. However, the productivity of photoautotrophic PHA production from cyanobacteria is much lower than in the case of heterotrophic bacteria. Great effort has been focused to reduce the cost of PHA production, mainly by the development of optimized strains and more efficient cultivation and recovery processes. Minimization of the PHA production cost can only be achieved by considering the design and a complete analysis of the whole process. With the aim on commercializing PHA, this review will discuss the advances and the challenges associated with the upstream processing of cyanobacterial PHA production, in order to help the design of the most efficient method on the industrial scale.

Direct detection of Exophiala and Scedosporium species in sputa of patients with cystic fibrosis

Detection of species of Exophiala and Scedosporium in the respiratory tracts of cystic fibrosis (CF) patients remains controversial because of highly variable results. The results of our study suggested a significantly higher prevalence and more complex colonization than previously estimated. Approximately 17% (27/162) of clinical sputum samples were found to be positive for Exophiala dermatitidis and 30% (49/162) were positive for Scedosporium apiospermum / S. boydii species complex determined by reverse line blot (RLB) hybridization. In contrast, only 14.2% (23/162) and 1.2% (2/162) of clinical sputa were positive for E. dermatitidis and S. apiospermum / S. boydii species complex when tested by culture, respectively. Molecular detection methods, such as loop-mediated isothermal amplification (LAMP) or reverse line blot (RLB) hybridization, have the potential to become powerful alternatives to selective culture, providing a more realistic understanding on the prevalence of E. dermatitidis and S. apiospermum / S. boydii species complex in the respiratory tract of CF patients.

Increased poly-β-hydroxybutyrate production from carbon dioxide in randomly mutated cells of cyanobacterial strain Synechocystis sp. PCC 6714: Mutant generation and characterization

Photosynthetic Poly-β-hydroxybutyrate (PHB) productivity in cyanobacteria needs to be increased to make cyanobacterial derived bioplastics economically feasible and competitive with petroleum-based plastics. In this study, high PHB yielding mutants of Synechocystis sp. PCC 6714 have been generated by random mutagenesis, using UV light as a mutagen. The selection of strains was based on PHB content induced by nitrogen and phosphorus starvation. The fast growing mutant MT_a24 exhibited more than 2.5-fold higher PHB productivity than that of the wild-type, attaining values of 37 ± 4% dry cell weight PHB. The MT_a24 was characterized for phenotypes, CO₂ uptake rate and gene expression levels using quantitative PCR. Genome sequencing showed that UV mutagenesis treatment resulted in a point mutation in the ABC-transport complex, phosphate-specific transport system integral membrane protein A (PstA). The MT_a24 shows potential for industrial production of PHB and also for carbon capture from the atmosphere or point sources.

Photosynthetic poly-β-hydroxybutyrate accumulation in unicellular cyanobacterium Synechocystis sp. PCC 6714

Poly-β-hydroxybutyrate (PHB) production from CO₂ has the potential to reduce the production cost of this biodegradable polyesters, and also to make the material more sustainable compared to utilization of sugar feedstocks. In this study the unicellular cyanobacterium, Synechocystis sp. PCC 6714 has been identified as an unexplored potential organism for production of PHB. Synechocystis sp. PCC 6714 was studied under various cultivation conditions and nutritional limitations. Combined effects of nitrogen and phosphorus deficiency led to highest PHB accumulation under photoautotrophic conditions. Multivariate experimental design and quantitative bioprocess development methodologies were used to identify the key cultivation parameters for PHB accumulation. Biomass growth and PHB accumulation were studied under controlled defined conditions in a lab-scale photobioreactor. Specific growth rates were fourfold higher in photobioreactor experiments when cultivation conditions were controlled. After 14 days of cultivation in nitrogen and phosphorus, limited media intracellular PHB levels reached up to 16.4% from CO₂. The highest volumetric production rate of PHB was 59 ± 6 mg L⁻¹ day⁻¹. Scanning electron microscopy of isolated PHB granules of Synechocystis sp. PCC 6714 cultivated under nitrogen and phosphorus limitations showed an average diameter of 0.7 µm. The results of this study might contribute towards a better understanding of photoautotrophic PHB production from cyanobacteria.

A prospective international Aspergillus terreus survey: an EFISG, ISHAM and ECMM joint study

OBJECTIVES

A prospective international multicentre surveillance study was conducted to investigate the prevalence and amphotericin B susceptibility of Aspergillus terreus species complex infections.

METHODS

A total of 370 cases from 21 countries were evaluated.

RESULTS

The overall prevalence of A. terreus species complex among the investigated patients with mould-positive cultures was 5.2% (370/7116). Amphotericin B MICs ranged from 0.125 to 32 mg/L, (median 8 mg/L).

CONCLUSIONS

Aspergillus terreus species complex infections cause a wide spectrum of aspergillosis and the majority of cryptic species display high amphotericin B MICs.

Real-time monitoring of beta-d-glucuronidase activity in sediment laden streams: A comparison of prototypes

Detection of enzymatic activities has been proposed as a rapid surrogate for the culture-based microbiological pollution monitoring of water resources. This paper presents the results of tests on four fully automated prototype instruments for the on-site monitoring of beta-d-glucuronidase (GLUC) activity. The tests were performed on sediment-laden stream water in the Hydrological Open Air Laboratory (HOAL) during the period of March 2014 to March 2015. The dominant source of faecal pollution in the stream was swine manure applied to the fields within the catchment. The experiments indicated that instrument pairs with the same construction design yielded highly consistent results (R(2) = 0.96 and R(2) = 0.94), whereas the results between different designs were less consistent (R(2) = 0.71). Correlations between the GLUC activity measured on-site and culture-based Escherichia coli analyses over the entire study period yielded R(2) = 0.52 and R(2) = 0.47 for the two designs, respectively. The correlations tended to be higher at the event scale. The GLUC activity was less correlated with suspended sediment concentrations than with E. coli, which is interpreted in terms of indicator applicability and the time since manure application. The study shows that this rapid assay can yield consistent results over a long period of on-site operation in technically challenging habitats. Although the use of GLUC activity as a proxy for culture-based assays could not be proven for the observed habitat, the study results suggest that this biochemical indicator has high potential for implementation in early warning systems.

Abstract PD6-03: High prevalence and clonal heterogeneity of ESR1 mutations (mt) in circulating tumor DNA (ctDNA) from patients (pts) enrolled in FERGI, a randomized phase II study testing pictilisib (GDC-0941) in combination with fulvestrant (F) in pts that failed a prior aromatase inhibitor (AI)

Background: Mutations in the ligand binding domain of the estrogen receptor gene (ESR1) have been associated with resistance to AI therapy in pts with ER+ breast cancer. To assess if ESR1 status has prognostic or predictive significance in the post-AI metastatic setting ESR1 mutation status was analyzed in circulating tumor DNA (ctDNA) from 168 pts enrolled on the FERGI study (NCT01437566; Krop et al., SABCS 2014).

Methods: Baseline and longitudinal mutational analysis for hotspot mutations in ESR1 (E380Q, S463P, V534E, P535H, L536R/H/P, L536Q, Y537N/S/C, D538G) and PIK3CA (C420R, E542K, E545K/G, Q546K, M1043I, H1047Y/R/L) was performed using droplet digital PCR (ddPCR) on ctDNA derived from plasma. Archival tissue was analyzed via RT-PCR and ddPCR.

Results: Baseline ctDNA analysis demonstrated a total of 62/156 (40%) and 57/153 (37%) pts with PIK3CA and ESR1 mutations, respectively. The most common ESR1 mutations are D538G, Y537S, and E380Q, representing 54%, 33% and 26% of the pts with a detectable ESR1 mutation at baseline, respectively. There was a numeric increase of ESR1 mutations in patients with LumA (41/99, 41%) vs LumB disease (14/44, 31%). PIK3CA mutations in asynchronously collected archival tissue were 85% concordant with plasma ctDNA mutations (sensitivity 78%, specificity 91%). PIK3CA mutations in baseline ctDNA showed a higher median allele frequency (AF) than ESR1 mutations (3.6% vs 0.46%), consistent with PIK3CA being an early event and ESR1 mutations occurring later in pts with recurrent disease. Of the pts with a detectable ESR1 mutation at baseline (n=57), 23 (40%) pts had multiple ESR1 mutations and 10 (18%) had ≥3 ESR1 mutations. The PFS outcomes for patients with and without ESR1 mutations detected at baseline are summarized below, indicating no obvious prognostic or predictive effect for combination of F with pictilisib compared with F in these underpowered subsets.

ArmESR1 MT - mPFS (mo)ESR1 WT - mPFS (mo)HR (95% CI)F + placebo5.4 (30 pts, 24 events)3.7 (40 pts, 31 events)1.06 (0.62, 1.81)F+pictilisib5.8 (27 pts, 20 events)6.7 (56 pts, 34 events)1.36 (0.78, 2.38)

PIK3CA and ESR1 ctDNA analysis on serial plasma samples from 40 pts and the assessment of ESR1 mutation status in the patient's tumor sample by ddPCR is currently in progress and will be reported.

Conclusions: Mutations in ESR1 detected by ddPCR in patient plasma samples occur in nearly 40% of pts that failed a prior AI. The polyclonal nature of ESR1 mutations is consistent with the convergent evolution of multiple AI resistant subclones. While these conclusions should be interpreted with caution due to the relatively small sample size and post hoc nature of the analysis, this data does not support a prognostic or predictive PFS hypothesis for ESR1 mutations with F or in combination with pictilisib.

Citation Format: Spoerke J, Gendreau S, Johnston S, Schmid P, Krop I, Qui J, Derynck M, Chan I, Walter K, Amler L, Hampton G, Lackner M. High prevalence and clonal heterogeneity of ESR1 mutations (mt) in circulating tumor DNA (ctDNA) from patients (pts) enrolled in FERGI, a randomized phase II study testing pictilisib (GDC-0941) in combination with fulvestrant (F) in pts that failed a prior aromatase inhibitor (AI). [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr PD6-03.

Geographically predominant genotypes of Aspergillus terreus species complex in Austria: s microsatellite typing study

Aspergillus terreus species complex is recognized as a frequent agent of invasive aspergillosis in Tyrol. The reason for this specific epidemiological situation is unclear. Aspergillus terreus strains isolated from environmental and clinical sources were genotyped using a novel panel of short tandem repeats and were evaluated for virulence. Three major endemic genotypes collected from the Inn region and its side valleys were found to cause the majority of invasive A. terreus infections. All of these genotypes were of the same mating type, which suggests that a mating barrier is present between these geographically well-adapted strains which is found to persist for at least 11 years. The three major genotypes were prevalent in both human infections and the environment. No major differences in virulence were observed using Galleria mellonella as model. Our data suggest a specific environmental exposure being responsible for the high incidence of A. terreus infections in Innsbruck, the Inn valley and side valleys (Tyrol, Austria).

Identification of Endoglin as an epigenetically regulated tumour-suppressor gene in lung cancer

Background:

The transforming growth factor-beta (TGF- β) pathway has been implicated in proliferation, migration and invasion of various cancers. Endoglin is a TGF-β accessory receptor that modulates signalling. We identified Endoglin as an epigenetically silenced tumour-suppressor gene in lung cancer by means of a genome-wide screening approach, then sought to characterise its effect on lung cancer progression.

Methods:

Methylation microarray and RNA sequencing were carried out on lung cancer cell lines. Epigenetic silencing of Endoglin was confirmed by methylation and expression analyses. An expression vector and a 20-gene expression panel were used to evaluate Endoglin function. Pyrosequencing was carried out on two independent cohorts comprising 112 and 202 NSCLC cases, respectively, and the impact of Endoglin methylation on overall survival (OS) was evaluated.

Results:

Methylation in the promoter region resulted in silencing of Endoglin, which could be reactivated by demethylation. Increased invasion coupled with altered EMT marker expression was observed in cell lines with an epithelial-like, but not those with a mesenchymal-like, profile when Endoglin was absent. Methylation was associated with decreased OS in stage I but not in stages II–III disease.

Conclusions:

We show that Endoglin is a common target of epigenetic silencing in lung cancer. We reveal a link between Endoglin silencing and EMT progression that might be associated with decreased survival in stage I disease.

ESCMID and ECMM joint guidelines on diagnosis and management of hyalohyphomycosis: Fusarium spp., Scedosporium spp. and others

Mycoses summarized in the hyalohyphomycosis group are heterogeneous, defined by the presence of hyaline (non-dematiaceous) hyphae. The number of organisms implicated in hyalohyphomycosis is increasing and the most clinically important species belong to the genera Fusarium, Scedosporium, Acremonium, Scopulariopsis, Purpureocillium and Paecilomyces. Severely immunocompromised patients are particularly vulnerable to infection, and clinical manifestations range from colonization to chronic localized lesions to acute invasive and/or disseminated diseases. Diagnosis usually requires isolation and identification of the infecting pathogen. A poor prognosis is associated with fusariosis and early therapy of localized disease is important to prevent progression to a more aggressive or disseminated infection. Therapy should include voriconazole and surgical debridement where possible or posaconazole as salvage treatment. Voriconazole represents the first-line treatment of infections due to members of the genus Scedosporium. For Acremonium spp., Scopulariopsis spp., Purpureocillium spp. and Paecilomyces spp. the optimal antifungal treatment has not been established. Management usually consists of surgery and antifungal treatment, depending on the clinical presentation.

Positions and numbers of FKS mutations in Candida albicans selectively influence in vitro and in vivo susceptibilities to echinocandin treatment

Candidemia is the fourth most common kind of microbial bloodstream infection, with Candida albicans being the most common causative species. Echinocandins are employed as the first-line treatment for invasive candidiasis until the fungal species is determined and confirmed by clinical diagnosis. Echinocandins block the FKS glucan synthases responsible for embedding β-(1,3)-d-glucan in the cell wall. The increasing use of these drugs has led to the emergence of antifungal resistance, and elevated MICs have been associated with single-residue substitutions in specific hot spot regions of FKS1 and FKS2. Here, we show for the first time the caspofungin-mediated in vivo selection of a double mutation within one allele of the FKS1 hot spot 1 in a clinical isolate. We created a set of isogenic mutants and used a hematogenous murine model to evaluate the in vivo outcomes of echinocandin treatment. Heterozygous and homozygous double mutations significantly enhance the in vivo resistance of C. albicans compared with the resistance seen with heterozygous single mutations. The various FKS1 hot spot mutations differ in the degree of their MIC increase, substance-dependent in vivo response, and impact on virulence. Our results demonstrate that echinocandin EUCAST breakpoint definitions correlate with the in vivo response when a standard dosing regimen is used but cannot predict the in vivo response after a dose escalation. Moreover, patients colonized by a C. albicans strain with multiple mutations in FKS1 have a higher risk for therapeutic failure.

Abstract P6-09-01: Central Ki67 analysis as a predictor for adjuvant capecitabine efficacy in early breast cancer (EBC) subtypes in US oncology trial 01062

Background: USON 01062 (O’Shaughnessy J, et al. Proc SABCS, 2010, abst S4-2) showed no improvement in the primary endpoint of disease-free survival (DFS) (median FU 5 yrs: HR 0.84, 95% CI: 0.67-1.05; p = 0.125) with the addition of capecitabine (X) to standard adjuvant chemotherapy, but showed improvement in OS (HR 0.68, 95% CI: 0.51-0.92; p = 0.011). Exploratory analysis of local pathology-assessed Ki67 suggested benefit from adjuvant X in pts with more highly proliferative cancers with Ki67 ≥ 10% (Pippen J et al. Proc ASCO, 2011, abst 500). The objective of this study is to determine whether centrally-performed Ki67 IHC results corroborate or refute this finding.

Methods: 2610 pts with resected high risk EBC were randomized to receive 4 cycles of AC (doxorubicin 60mg/m2 and cyclophosphamide 600mg/m2) IV every 3 wks for 4 cycles followed by either docetaxel 100mg/m2 IV or docetaxel 75mg/m2 IV plus X 825mg/m2 PO bid for 14 days every 3 wks for 4 cycles. Archival primary breast cancer tissue was collected on 2000 pts for predictive biomarker analyses. Central Ki67 IHC was performed using the anti-Ki67 monoclonal antibody SP6 and was read by one pathologist (HK) according to published recommendations (Dowsett M, et al. JNCI 103:1-9, 2011).

Results: Central Ki67 IHC has been performed on 1440 pts who had centrally-validated informed consents. The distribution of% Ki67-positive cells by locally-assessed ER/HER2 subtype is shown below. 45% of HR+ HER2- BCs had a Ki67 ≤ 10%, while 24% had a Ki67 11% to 20%, and 31% had a Ki67 > 20%. The concordance between the local vs central Ki67 results was low at 46% for Ki67 <10%, 49% for Ki67 10%-20%, and 76% for Ki67 > 20%. The central Ki67 results tended to be higher than the local testing results. Central mRNA classifiers were developed for ER, PR, HER2 and Ki67 using Fluidigm Microfluidics Dynamic Arrays and correlate highly with central IHC assessment of these markers.

Conclusions: HR+ HER2- EBC is enriched for cancers with a low proliferative rate, a group of pts unlikely to benefit from the cell cycle-specific cytotoxic agent, capecitabine. Analyses of the impact of adjuvant X added to AC/T in EBC pts according to ER status, and according to Ki67 (analyzed as a binary and continuous variable) will be performed prior to SABCS, 2013.

Number of Patients% Ki67 Pos CellsTotal *HR+TNHER2+/HR+HER2+/ HR-0-104163622222711-151391066151016-20126871615821-3018411539201031-1005751403423555Total144081042510790*Totals do not equal sum of subtype categories due to missing HER2 information

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-09-01.

Abstract P4-06-10: Epigenetic silencing of glutamine synthetase (Glul) defines glutamine depletion therapy

Background: Methylation-dependent transcriptional silencing of genes involved in amino acid synthesis can provide potential targets for novel synthetic lethality strategies. Glutamine synthetase (Glul) is the key enzyme in the biosynthesis of glutamine. We identified Glul as a novel gene subject to methylation-dependent transcriptional silencing in breast cancer cell lines using a combined functional screen with methylation reversal assays and methylation arrays.

Methods: Methylation reversal assays were performed using 5-aza-2-deoxycytidine and/or trichostatin treatment coupled with whole genome mRNA microarrays (Illumina HT-12 v4 Expression BeadChip Kit). Expression of Glul with and without pharmacological methylation reversal with azacytidine and/or trichostatin was validated using qRT-PCR and Western Blot. Methylation of Glul was analysed using methylation microarrays (Illumina 450K Methylation BeadChip), bisulphite sequencing and pyrosequencing. Sensitivity to glutamine deprivation was assessed using an MTT assay after culturing cells in media with various glutamine concentrations or in complete absence of glutamine. We used a panel of 55 breast cancer cell lines and formalin-fixed paraffin-embedded tissue from a series of 116 stage I-III primary breast cancers with linked mature clinical outcome data that were randomly selected from the Cuneo Tissue Bank. Tissue samples were subject to histopathological review to ensure adequate representation of cancer cells.

Results: Dense methylation of the CpG-island of Glul was detected in 45% of cell lines across all subtypes. Methylation of the CpG island was linked with absent or down-regulated expression of Glul in some but not all cell lines, and Glul expression could be reactivated by azacytidine and trichostatin in these cell lines. Methylation of shore areas was detected in several cell lines but was not associated with transcriptional silencing. Cells with methylation-dependent low or absent Glul expression were highly sensitive to glutamine deprivation, whereas cell lines without Glul methylation were rescued by compensatory up-regulation of Glul. Using pyrosequencing, dense methylation of the CpG island of Glul was found in 32.8% of patients, with an additional 17.2% of patients showing partial methylation. No significant association with a specific breast cancer subtype or outcome was found.

Conclusions: This is the first report of methylation-dependent transcriptional silencing of Glul expression in cancer. Our data demonstrate that a significant proportion of primary breast cancers show methylation of Glul and suggest that glutamine deprivation could be a novel synthetic lethality strategy for these cancers.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-06-10.

Infection and colonisation due to Scedosporium in Northern Spain. An in vitro antifungal susceptibility and molecular epidemiology study of 60 isolates

Since the latest taxonomical changes in the genus Scedosporium by Gilgado et al. in 2010, no species-specific studies on epidemiology and antifungal susceptibility patterns (AFSP) have so far been published. This study aimed to provide qualitative epidemiological data of Scedosporium spp. isolated from cystic fibrosis (CF) patients and immunocompromised patients from Northern Spain. Isolates were identified by using amplified fragment length polymorphism (AFLP), and species-specific AFSP were generated for all currently available antifungal compounds. AFLP was a useful tool for identification to species-level and for the discrimination of inter- and intra-patient isolates. Scedosporium prolificans represents the most prevalent species in the respiratory tract of CF patients and immunocompromised patients in Northern-Spain, followed by Pseudallescheria boydii, P. apiosperma, and P. ellipsoidea. CF patients were exclusively colonised with either P. boydii or S. prolificans. Patients were colonised over years exclusively with isolates affiliated to one species, but some patients were colonised with multiple strains with different AFSP. The sum of those co-colonising strains in one patient, may appear in vitro and in vivo as a multi-resistant S. prolificans isolate, as strains are morphologically identical and might therefore be regarded as only one strain. A majority of Scedosporium strains (with exception of S. prolificans) were found susceptible for voriconazole and micafungin.

Severe prosthetic joint infection in an immunocompetent male patient due to a therapy refractory Pseudallescheria apiosperma

Prosthetic joint infections (PJI) are rarely due to fungal agents and if so they are mainly caused by Candida strains. This case represents a PJI caused by a multi-drug resistant Pseudallescheria apiosperma, with poor in vivo response to itraconazole and voriconazole. This case differs also by the way of infection, since the joint infection did not follow a penetrating trauma. In the majority of cases, Scedosporium extremity infections remain local in immunocompetent individuals. We report a persistent joint infection with multiple therapeutic failures, and subsequent amputation of the left leg. Detailed clinical data, patient history, treatment regime and outcome of a very long-lasting (>4 years) P. apiosperma prosthetic knee infection in an immunocompetent, 61-year-old male patient are presented with this case. The patient was finally cured by the combination of multiple and extensive surgical interventions and prolonged antifungal combination therapy with voriconazole and terbinafine.