D 5.5.1.1. Final report on sensory testing in Africa for Group 1. Project AFTER “African Food Tradition rEvisited by Research”

This deliverable concerns the sensory evaluation of the reengineered group 1 African products in the AFTER project. Specifically, it related to reengineered akpan and gowe from Benin, kenkey from Ghana and Kishk Sa'eedi in Egypt. Concerning reengineered akpan from Benin, the sensory evaluation was undertaken in Montpellier, France. Re-engineering of akpan has focused primarily on improvement of sanitary properties of the product, which was a great achievement and will allow producing Akpan on a larger scale in SMEs in Africa. Sensory evaluation of the Akpan products was carried out using CATA and JAR techniques that have been developed for use with consumers instead of a trained panel. Three Akpan products were tested by 102 consumers: Akpan added with 10% sugar (AS10), Akpan added with 3% spray-dried milk and 8.7% sugar (AMS8.7) and Akpan added with 3% spray-dried milk and 15% sugar (AMS15). Independently of the Akpan tasted, Acidity or Sweetness attributes were scored “Just About Right, as I like” by 56 to 77% of consumers. Odour perception was perceived differently, depending on consumers. However, Texture was found “Too weak”, too liquid by the majority of consumers (49 to 55%) and Taste “too strong” (46 to 54%). The most frequently CATA descriptors checked by consumers which better described Akpan products were: “Artificial”, “Floral”, “New/Different”, “Strong in Taste”, “Mealy”, followed by “Liquid”, “Drinking yoghurt”, “Sweet”, “Acidic”, and “Rough”. At the opposite, an ideal-yoghurt was described as Creamy, Natural, Good for health, Refreshing, Homogeneous, with a texture of a Bulgarian yoghurt-type, Thick, Sweet, Attractive, Nutritious and Milk taste. In terms of sensory evaluation, the three Akpan products did not significantly. If we remove the terms such as “artificial”, “strong in taste”, “floral” due to a manufacturing error (use of a few drops of citronella essential oil instead of citronella infusion as a traditional flavouring of Akpan in Benin), it remains the terms “mealy”, “liquid” “drinking yoghurt” that better describe the product and were previously used for describing traditional Akpan product. This suggests that sensory properties of the reengineered Akpan may not be acceptable to French consumers who prefer a product with a creamy, homogeneous, Bulgarian yoghurt-type taste. Gowe in Benin was not tested using sensory evaluation. Sensory testing of Gowe in Benin was not undertaken because this was planned to be undertaken in Europe. The reason is because the methodology used in sensory evaluation is independent of the location provided the samples are the same. However, the particular samples provided for French sensory testing contained a concentration of aflatoxin that was higher than the minimum EU allowable limit. It was not possible to repeat the sensory test in France because it would have taken too long to obtain a replacement supply from Benin and to repeat the processing (takes one week). In which case the samples would have been took different to enable a comparison. The sensory evaluation of kenkey was carried at the Food Research Institute, Ghana. Current trends in urbanization, and the increasing popularity of kenkey among consumers, require larger scale production with consistent quality. Testing was conducted to determine the sensory profile of white reengineered kenkey made using the optimum pre-process conditions of steeping time (30 and 45h), steeping temperature (30ᵒC and 35ᵒC) and dough fermentation time of 12 hours. The qualitative descriptive analysis showed that the sensory profile of white kenkey was dependent on preprocessing variables. Thus merely optimizing the pre-processing variables with regards to acid production and other readily measurable constituents though could shorten the production process could not guarantee the best product sensory quality. The results show that all the descriptors generated were appropriate for differentiating sensory qualities among samples and could be used for basic research and product development for white kenkey. Soft and sticky texture in white kenkey was highly appreciated. Sensory evaluation of Kishk Sa'eedi (KS) was undertaken in Egypt. KS is an Egyptian indigenous wheat-based fermented food prepared traditionally according to the method applied by Upper Egyptians. This work is done to characterize sensory properties and sensory profile of the reengineered KS. Quantitative descriptive analysis (QDA) coupled with principal component analysis (PCA) was used to study the interrelationship among and between sensory attributes. 14 terms regarding appearance, odour, flavour and texture of the samples, was selected and a glossary describing each descriptor was developed. Three KS samples were profiled by 11 assessors using the chosen 14 sensory descriptors. Mean intensity ratings of the descriptive attributes showed that there were significant differences (p<0.05) within KS samples for all the 14 attributes tested. In general, high ratings for creamy colour, fresh odour, KS taste and fracturability are considered as positive effects that would be favoured by panellists while increase in caramel colour, sour taste, denseness and mouth coating are regarded as undesirable. The re-engineered KS sample perceived as less sour and less salty compared with the traditional ones. With regard to texture quality, reengineered sample was easy to fracture, and scored higher for grittiness. Meanwhile, the sample was rated lower than the traditional ones with regard to Kishk taste and fermented odour. Descriptive sensory evaluations between of the traditional and re-engineered KS samples showed that tastes i.e. sour, salty, and KS taste; fracutability and grittiness were discriminating attributes. Fermented odour, colour i.e. creamy and caramel; presence of fissure and presence of bran were least discriminating. Evaluation of the KS sensory characteristics provide in depth understanding of the sensory quality criteria as perceived by the sensory trained panel. The present study showed that substantial differences in sensory character were noted between the traditional and re-engineered KS in particular, differences in colour, fresh odour, KS taste, fracutability and mouth coating. This work showed that the application of QFD and PCA techniques could provide the useful information to KS and helped to identify the importance of product attributes. In conclusion the sensory evaluation showed clear sensory differences between the traditional and reengineered products relating to akpan from Benin, kenkey from Ghana and Kishk Sa'eedi from Egypt. Other deliverables will report on the acceptance by consumers

Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy.

Current cell-free DNA (cfDNA) next generation sequencing (NGS) precision oncology workflows are typically limited to targeted and/or disease-specific applications. In advanced cancer, disease burden and cfDNA tumor content are often elevated, yielding unique precision oncology opportunities. We sought to demonstrate the utility of a pan-cancer, rapid, inexpensive, whole genome NGS of cfDNA approach (PRINCe) as a precision oncology screening strategy via ultra-low coverage (~0.01x) tumor content determination through genome-wide copy number alteration (CNA) profiling. We applied PRINCe to a retrospective cohort of 124 cfDNA samples from 100 patients with advanced cancers, including 76 men with metastatic castration-resistant prostate cancer (mCRPC), enabling cfDNA tumor content approximation and actionable focal CNA detection, while facilitating concordance analyses between cfDNA and tissue-based NGS profiles and assessment of cfDNA alteration associations with mCRPC treatment outcomes. Therapeutically relevant focal CNAs were present in 42 (34%) cfDNA samples, including 36 of 93 (39%) mCRPC patient samples harboring AR amplification. PRINCe identified pre-treatment cfDNA CNA profiles facilitating disease monitoring. Combining PRINCe with routine targeted NGS of cfDNA enabled mutation and CNA assessment with coverages tuned to cfDNA tumor content. In mCRPC, genome-wide PRINCe cfDNA and matched tissue CNA profiles showed high concordance (median Pearson correlation = 0.87), and PRINCe detectable AR amplifications predicted reduced time on therapy, independent of therapy type (Kaplan-Meier log-rank test, chi-square = 24.9, p &lt; 0.0001). Our screening approach enables robust, broadly applicable cfDNA-based precision oncology for patients with advanced cancer through scalable identification of therapeutically relevant CNAs and pre-/post-treatment genomic profiles, enabling cfDNA- or tissue-based precision oncology workflow optimization

Spontaneous development of Epstein-Barr Virus associated human lymphomas in a prostate cancer xenograft program

Prostate cancer research is hampered by the lack of in vivo preclinical models that accurately reflect patient tumour biology and the clinical heterogeneity of human prostate cancer. To overcome these limitations we propagated and characterised a new collection of patient-derived prostate cancer xenografts. Tumour fragments from 147 unsupervised, surgical prostate samples were implanted subcutaneously into immunodeficient Rag2-/-γC-/- mice within 24 hours of surgery. Histologic and molecular characterisation of xenografts was compared with patient characteristics, including androgen-deprivation therapy, and exome sequencing. Xenografts were established from 47 of 147 (32%) implanted primary prostate cancers. Only 14% passaged successfully resulting in 20 stable lines; derived from 20 independent patient samples. Surprisingly, only three of the 20 lines (15%) were confirmed as prostate cancer; one line comprised of mouse stroma, and 16 were verified as human donor-derived lymphoid neoplasms. PCR for Epstein-Barr Virus (EBV) nuclear antigen, together with exome sequencing revealed that the lymphomas were exclusively EBV-associated. Genomic analysis determined that 14 of the 16 EBV+ lines had unique monoclonal or oligoclonal immunoglobulin heavy chain gene rearrangements, confirming their B-cell origin. We conclude that the generation of xenografts from tumour fragments can commonly result in B-cell lymphoma from patients carrying latent EBV. We recommend routine screening, of primary outgrowths, for latent EBV to avoid this phenomenon

Fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin with gemtuzumab ozogamicin improves event-free survival in younger patients with newly diagnosed aml and overall survival in patients with npm1 and flt3 mutations

Purpose To determine the optimal induction chemotherapy regimen for younger adults with newly diagnosed AML without known adverse risk cytogenetics. Patients and Methods One thousand thirty-three patients were randomly assigned to intensified (fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin [FLAG-Ida]) or standard (daunorubicin and Ara-C [DA]) induction chemotherapy, with one or two doses of gemtuzumab ozogamicin (GO). The primary end point was overall survival (OS). Results There was no difference in remission rate after two courses between FLAG-Ida + GO and DA + GO (complete remission [CR] + CR with incomplete hematologic recovery 93% v 91%) or in day 60 mortality (4.3% v 4.6%). There was no difference in OS (66% v 63%; P = .41); however, the risk of relapse was lower with FLAG-Ida + GO (24% v 41%; P < .001) and 3-year event-free survival was higher (57% v 45%; P < .001). In patients with an NPM1 mutation (30%), 3-year OS was significantly higher with FLAG-Ida + GO (82% v 64%; P = .005). NPM1 measurable residual disease (MRD) clearance was also greater, with 88% versus 77% becoming MRD-negative in peripheral blood after cycle 2 (P = .02). Three-year OS was also higher in patients with a FLT3 mutation (64% v 54%; P = .047). Fewer transplants were performed in patients receiving FLAG-Ida + GO (238 v 278; P = .02). There was no difference in outcome according to the number of GO doses, although NPM1 MRD clearance was higher with two doses in the DA arm. Patients with core binding factor AML treated with DA and one dose of GO had a 3-year OS of 96% with no survival benefit from FLAG-Ida + GO. Conclusion Overall, FLAG-Ida + GO significantly reduced relapse without improving OS. However, exploratory analyses show that patients with NPM1 and FLT3 mutations had substantial improvements in OS. By contrast, in patients with core binding factor AML, outcomes were excellent with DA + GO with no FLAG-Ida benefit

Induction of anti-apoptotic factors by cutaneous Human Papillomaviruses

Human Papillomaviruses (HPVs) are small DNA viruses which specifically infect keratinocytes at different body sites. An association between cutaneous Squamous Cell Carcinoma (SCC) formation, UV irradiation and infection with a high-risk subset of cutaneous HPVs has been postulated although the underlying molecular mechanisms by which HPV may play a role in SCC development are not yet fully elucidated. Expression of the viral E6 oncoprotein has been shown to interfere with DNA damage responses and inhibit UV induced apoptosis, suggesting HPV can contribute to early stages in tumourigenesis. Here, expression of E6 from HPV types 5, 8, 10, 18 and 77 was shown to reduce UV- or Fas-induced apoptosis, and the changes in a range of intracellular apoptotic regulators were investigated. Additionally, the subject of cutaneous SCCs, in contrast to HPV-associated anogenital cancers, not harboring HPV DNA in every tumor cell was explored. Results herein show that expression of E6 from skin cancer-associated HPV types 5 and 8 induced the secretion of factors that were able to inhibit UV-induced apoptosis in non-HPV expressing cell lines and primary human keratinocytes. The anti-apoptotic effect of HPV E6 expression was found to be mediated in part by upregulation of Osteoprotegerin (OPG) and Interleukin 6 (IL6). Purified OPG and IL6, when added to cells together, but not individually, reduced apoptosis following UV irradiation. Evidence is shown that OPG and IL6 inhibit the extrinsic and intrinsic apoptotic pathways respectively. Furthermore immunohistochemistry of HPV-typed SCC sections shows that IL6 protein is up-regulated in HPV positive tumors compared to HPV-negative cancers. To further test the effects of HPV5E6 expression, in combination with UV irradiation, on primary human keratinocytes microarray studies were performed. These findings support the hypothesis that a small number of HPV infected cells influence UV induced apoptosis in the skin and contribute to tumourigenesis