Identification of a HIV-1 circulating BF1 recombinant form (CRF75_BF1) of Brazilian origin that also circulates in Southwestern Europe

Introduction

The high recombinogenic potential of HIV-1 has resulted in the generation of countless unique recombinant forms (URFs) and around 120 reported circulating recombinant forms (CRFs). Here we identify through analyses of near full-length genomes (NFLG) a new HIV-1 CRF derived from subtypes B and F1.

Methods

HIV-1 protease-reverse transcriptase (Pr-RT) sequences were obtained by RT-PCR amplification from plasma RNA. Near full-length genome sequences were obtained after amplification by RT-PCR in 5 overlapping fragments. Phylogenetic sequence analyses were performed via maximum likelihood. Mosaic structures were analyzed by bootscanning and phylogenetic analyses of genome segments. Temporal and geographical estimations of clade emergence were performed with a Bayesian coalescent method.

Results

Through phylogenetic analyses of HIV-1 Pr-RT sequences obtained by us from samples collected in Spain and downloaded from databases, we identified a BF1 recombinant cluster segregating from previously reported CRFs comprising 52 viruses, most from Brazil (n = 26), Spain (n = 11), and Italy (n = 9). The analyses of NFLG genomes of 4 viruses of the cluster, 2 from Spain and 2 from Italy, allowed to identify a new CRF, designated CRF75_BF1, which exhibits a complex mosaic structure with 20 breakpoints. All 4 patients harboring CRF75_BF1 viruses studied by us had CD4+ T-cell lymphocyte counts below 220/mm3 less than one year after diagnosis, a proportion significantly higher (p = 0.0074) than the 29% found in other patients studied in Spain by us during the same period. The origin of the clade comprising CRF75_BF1 and related viruses was estimated around 1984 in Brazil, with subsequent introduction of CRF75_BF1 in Italy around 1992, and migration from Italy to Spain around 1999.

Conclusion

A new HIV-1 CRF, designated CRF75_BF1, has been identified. CRF75_BF1 is the 6th CRF of South American origin initially identified in Western Europe, reflecting the increasing relationship of South American and European HIV-1 epidemics. The finding of low CD4+ T-cell lymphocyte counts early after diagnosis in patients harboring CRF75_BF1 viruses warrants further investigation on the virulence of this variant.

Factors associated with HIV-1 resistance to integrase strand transfer inhibitors in Spain: Implications for dolutegravir-containing regimens

Integrase strand transfer inhibitor (INSTI)-containing regimens in HIV-1-infected patients have experienced a global increase. Recently, WHO has emphasized the need to fast-track the transition to dolutegravir (DTG)-based antiretroviral (ARV) treatments. However, continued surveillance of INSTI resistance is recommended. In this study, clinical, epidemiological, and virological features associated with INSTI resistance diagnosed in Spain were analyzed. Samples collected between 2008 and 2021 from HIV-1-infected patients were analyzed in integrase, protease, and reverse transcriptase using Sanger population sequencing. ARV drug resistance was evaluated with the Stanford University HIVdb program. Among 2,696 patients, 174 (6.5%) had INSTI resistance, all of them to first-generation INSTIs, and 71 (2.6%) had also resistance to second-generation INSTIs. Of these, only 5 individuals were exposed to DTG as the only INSTI, in whom resistance development was associated with poor treatment adherence and/or resistance to other ARV classes. Of newly HIV-1-diagnosed individuals, 0.92% harbored INSTI-resistant viruses, with low prevalences maintained along time, and only one had low-level resistance to DTG. Persons who inject drugs, age over 39 years, resistance to other ARV classes, and longer time from diagnosis were associated with INSTI resistance (p < 0.001). Non-subtype B INSTI-resistant viruses lacked the Q148H + G140S resistance pathway and showed lower INSTI resistance levels than subtype B viruses. In conclusion, INSTI resistance is uncommon and associated with long-term infections, older age and additional resistance to other ARV drug classes, and is rare in newly diagnosed HIV-1 infections. Our results also support the preferential use of DTG-containing regimens in first-line treatments, although surveillance of INSTI resistance is encouraged.

Pembrolizumab in combination with gemcitabine for patients with HER2-negative advanced breast cancer: GEICAM/2015-04 (PANGEA-Breast) study

BACKGROUND

We evaluated a new chemoimmunotherapy combination based on the anti-PD1 monoclonal antibody pembrolizumab and the pyrimidine antimetabolite gemcitabine in HER2- advanced breast cancer (ABC) patients previously treated in the advanced setting, in order to explore a potential synergism that could eventually obtain long term benefit in these patients.

METHODS

HER2-negative ABC patients received 21-day cycles of pembrolizumab 200 mg (day 1) and gemcitabine (days 1 and 8). A run-in-phase (6 + 6 design) was planned with two dose levels (DL) of gemcitabine (1,250 mg/m² [DL0]; 1,000 mg/m² [DL1]) to determine the recommended phase II dose (RP2D). The primary objective was objective response rate (ORR). Tumor infiltrating lymphocytes (TILs) density and PD-L1 expression in tumors and myeloid-derived suppressor cells (MDSCs) levels in peripheral blood were analyzed.

RESULTS

Fourteen patients were treated with DL0, resulting in RP2D. Thirty-six patients were evaluated during the first stage of Simon's design. Recruitment was stopped as statistical assumptions were not met. The median age was 52; 21 (58%) patients had triple-negative disease, 28 (78%) visceral involvement, and 27 (75%) ≥ 2 metastatic locations. Progression disease was observed in 29 patients. ORR was 15% (95% CI, 5-32). Eight patients were treated ≥ 6 months before progression. Fourteen patients reported grade ≥ 3 treatment-related adverse events. Due to the small sample size, we did not find any clear association between immune tumor biomarkers and treatment efficacy that could identify a subgroup with higher probability of response or better survival. However, patients that experienced a clinical benefit showed decreased MDSCs levels in peripheral blood along the treatment.

CONCLUSION

Pembrolizumab 200 mg and gemcitabine 1,250 mg/m² were considered as RP2D. The objective of ORR was not met; however, 22% patients were on treatment for ≥ 6 months. ABC patients that could benefit of chemoimmunotherapy strategies must be carefully selected by robust and validated biomarkers. In our heavily pretreated population, TILs, PD-L1 expression and MDSCs levels could not identify a subgroup of patients for whom the combination of gemcitabine and pembrolizumab would induce long term benefit.

TRIAL REGISTRATION

ClinicalTrials.gov and EudraCT (NCT03025880 and 2016-001,779-54, respectively). Registration dates: 20/01/2017 and 18/11/2016, respectively.

The Origin, Epidemiology, and Phylodynamics of Human Immunodeficiency Virus Type 1 CRF47_BF

CRF47_BF is a circulating recombinant form (CRF) of the human immunodeficiency virus type 1 (HIV-1), the etiological agent of AIDS. CRF47_BF represents one of 19 CRFx_BFs and has a geographic focus in Spain, where it was first identified in 2010. Since its discovery, CRF47_BF has expanded considerably in Spain, predominantly through heterosexual contact (∼56% of the infections). Little is known, however, about the origin and diversity of this CRF or its epidemiological correlates, as very few samples have been available so far. This study conducts a phylogenetic analysis with representatives of all CRFx_BF sequence types along with HIV-1 M Group subtypes to validate that the CRF47_BF sequences share a unique evolutionary history. The CRFx_BF sequences cluster into a single, not well supported, clade that includes their dominant parent subtypes (B and F). This clade also includes subtype D and excludes sub-subtype F2. However, the CRF47_BF sequences all share a most recent common ancestor. Further analysis of this clade couples CRF47_BF protease-reverse transcriptase sequences and epidemiological data from an additional 87 samples collected throughout Spain, as well as additional CRF47_BF database sequences from Brazil and Spain to investigate the origin and phylodynamics of CRF47_BF. The Spanish region with the highest proportion of CRF47_BF samples in the data set was the Basque Country (43.7%) with Navarre next highest at 19.5%. We include in our analysis epidemiological data on host sex, mode of transmission, time of collection, and geographic region. The phylodynamic analysis indicates that CRF47_BF originated in Brazil around 1999–2000 and spread to Spain from Brazil in 2002–2003. The virus spread rapidly throughout Spain with an increase in population size from 2011 to 2015 and leveling off more recently. Three strongly supported clusters associated with Spanish regions (Basque Country, Navarre, and Aragon), together comprising 60.8% of the Spanish samples, were identified, one of which was also associated with transmission among men who have sex with men. The expansion in Spain of CRF47_BF, together with that of other CRFs and subtype variants of South American origin, previously reported, reflects the increasing relationship between the South American and European HIV-1 epidemics.

Viruses Previously Identified in Brazil as Belonging to HIV-1 CRF72_BF1 Represent Two Closely Related Circulating Recombinant Forms, One of Which, Designated CRF122_BF1, Is Also Circulating in Spain

Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Those derived from recombination between subtype B and subsubtype F1, with 18 reported, most of them of South American origin, are among the most diverse. In this study, we identified a HIV-1 BF1 recombinant cluster that is expanding in Spain, transmitted mainly via heterosexual contact, which, analyzed in near full-length genomes in four viruses, exhibited a coincident BF1 mosaic structure, with 12 breakpoints, that fully coincided with that of two viruses (10BR_MG003 and 10BR_MG005) from Brazil, previously classified as CRF72_BF1. The three remaining Brazilian viruses (10BR_MG002, 10BR_MG004, and 10BR_MG008) previously identified as CRF72_BF1 exhibited mosaic structures highly similar, but not identical, to that of the Spanish viruses and to 10BR_MG003 and 10BR_MG005, with discrepant subtypes in two short genome segments, located in pol and gp120^env. Based on these results, we propose that the five viruses from Brazil previously identified as CRF72_BF1 actually belong to two closely related CRFs, one comprising 10BR_MG002, 10BR_MG004, and 10BR_MG008, which keep their CRF72_BF1 designation, and the other, designated CRF122_BF1, comprising 10BR_MG003, 10BR_MG005, and the viruses of the identified Spanish cluster. Three other BF1 recombinant genomes, two from Brazil and one from Italy, previously identified as unique recombinant forms, were classified as CRF72_BF1. CRF122_BF1, but not CRF72_BF1, was associated with protease L89M substitution, which was reported to contribute to antiretroviral drug resistance. Phylodynamic analyses estimate the emergence of CRF122_BF1 in Brazil around 1987. Given their close phylogenetic relationship and similar structures, the grouping of CRF72_BF1 and CRF122_BF1 in a CRF family is proposed.

Transmission Clusters, Predominantly Associated With Men Who Have Sex With Men, Play a Main Role in the Propagation of HIV-1 in Northern Spain (2013–2018)

Viruses of HIV-1-infected individuals whose transmission is related group phylogenetically in transmission clusters (TCs). The study of the phylogenetic relations of these viruses and the factors associated with these individuals is essential to analyze the HIV-1 epidemic. In this study, we examine the role of TCs in the epidemiology of HIV-1 infection in Galicia and the Basque County, two regions of northern Spain. A total of 1,158 HIV-1-infected patients from both regions with new diagnoses (NDs) in 2013–2018 were included in the study. Partial HIV-1 pol sequences were analyzed phylogenetically by approximately maximum-likelihood with FastTree 2. In this analysis, 10,687 additional sequences from samples from HIV-1-infected individuals collected in Spain in 1999–2019 were also included to assign TC membership and to determine TCs’ sizes. TCs were defined as those which included viruses from ≥4 individuals, at least 50% of them Spaniards, and with ≥0.95 Shimodaira-Hasegawa-like node support in the phylogenetic tree. Factors associated to TCs were evaluated using odds ratios (OR) and their 95% CI. Fifty-one percent of NDs grouped in 162 TCs. Male patients (OR: 2.6; 95% CI: 1.5–4.7) and men having sex with men (MSM; OR: 2.1; 95% CI: 1.4–3.2) had higher odds of belonging to a TC compared to female and heterosexual patients, respectively. Individuals from Latin America (OR: 0.3; 95% CI: 0.2–0.4), North Africa (OR: 0.4; 95% CI: 0.2–1.0), and especially Sub-Saharan Africa (OR: 0.02; 95% CI: 0.003–0.2) were inversely associated to belonging to TCs compared to native Spaniards. Our results show that TCs are important components of the HIV-1 epidemics in the two Spanish regions studied, where transmission between MSM is predominant. The majority of migrants were infected with viruses not belonging to TCs that expand in Spain. Molecular epidemiology is essential to identify local peculiarities of HIV-1 propagation. The early detection of TCs and prevention of their expansion, implementing effective control measures, could reduce HIV-1 infections.

Identification of CRF66_BF, a New HIV-1 Circulating Recombinant Form of South American Origin

Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Among 110 reported in the literature, 17 are BF1 intersubtype recombinant, most of which are of South American origin. Among these, all 5 identified in the Southern Cone and neighboring countries, except Brazil, derive from a common recombinant ancestor related to CRF12_BF, which circulates widely in Argentina, as deduced from coincident breakpoints and clustering in phylogenetic trees. In a HIV-1 molecular epidemiological study in Spain, we identified a phylogenetic cluster of 20 samples from 3 separate regions which were of F1 subsubtype, related to the Brazilian strain, in protease-reverse transcriptase (Pr-RT) and of subtype B in integrase. Remarkably, 14 individuals from this cluster (designated BF9) were Paraguayans and only 4 were native Spaniards. HIV-1 transmission was predominantly heterosexual, except for a subcluster of 6 individuals, 5 of which were men who have sex with men. Ten additional database sequences, from Argentina (n = 4), Spain (n = 3), Paraguay (n = 1), Brazil (n = 1), and Italy (n = 1), branched within the BF9 cluster. To determine whether it represents a new CRF, near full-length genome (NFLG) sequences were obtained for 6 viruses from 3 Spanish regions. Bootscan analyses showed a coincident BF1 recombinant structure, with 5 breakpoints, located in p17^gag, integrase, gp120, gp41-rev overlap, and nef, which was identical to that of two BF1 recombinant viruses from Paraguay previously sequenced in NFLGs. Interestingly, none of the breakpoints coincided with those of CRF12_BF. In a maximum likelihood phylogenetic tree, all 8 NFLG sequences grouped in a strongly supported clade segregating from previously identified CRFs and from the CRF12_BF “family” clade. These results allow us to identify a new HIV-1 CRF, designated CRF66_BF. Through a Bayesian coalescent analysis, the most recent common ancestor of CRF66_BF was estimated around 1984 in South America, either in Paraguay or Argentina. Among Pr-RT sequences obtained by us from HIV-1-infected Paraguayans living in Spain, 14 (20.9%) of 67 were of CRF66_BF, suggesting that CRF66_BF may be one of the major HIV-1 genetic forms circulating in Paraguay. CRF66_BF is the first reported non-Brazilian South American HIV-1 CRF_BF unrelated to CRF12_BF.

Biological Deacidification Strategies for White Wines

Traditionally, the use of malolactic fermentation gives rise to microbiologically stable wines. However, malolactic fermentation is not free from possible collateral effects that can take place under specific scenarios. The present work tests the influence of different biological deacidification strategies on the volatile and non-volatile components of white must from Germany. The study compared mixed cultures of Lachancea thermotolerans and Schizosaccharomyces pombe and a pure culture of Sc. pombe to the classical biological deacidification process performed by lactic acid bacteria. Strains of Oenococcus oeni and Lactiplantibacillus plantarum were co- or sequentially inoculated with S. cerevisiae to carry out malolactic fermentation. Different fermentation treatments took place at a laboratory scale of 0.6 L in vessels of 0.75 L. The instrumental techniques Fourier-transform mid-infrared spectroscopy (FT-MIR), high performance liquid chromatography (HPLC) and gas chromatography–mass spectrometry (GC-MS) were used to evaluate different chemical parameters in the final wines. The results showed the ability of Sc. pombe to consume malic acid in combination with L. thermotolerans without using S. cerevisiae or lactic acid bacteria. Fermentations involving Sc. pombe consumed all the malic acid, although they reduced the concentrations of higher alcohols, fatty acids and acetic acid. Simultaneous alcoholic and malolactic fermentations reduced malic acid by about 80%, while classical malolactic fermentation reduced it by 100%. Fermentations involving L. thermotolerans produced the highest lactic acid, ester and glycerol concentrations.

Studying the properties of the Bitcoin as a diversifying and hedging asset through a copula analysis: Constant and time-varying

In this study, we analyze the properties of Bitcoin as a diversifier asset and hedge asset against the movement of international market stock indices: S&P500 (US), STOXX50 (EU), NIKKEI (Japan), CSI300 (Shanghai), and HSI (Hong Kong). For this, we use several copula models: Gaussian, Student-t, Clayton, Gumbel, and Frank. The analysis period runs from August 18, 2011 to June 31, 2019. We found that the Gaussian and Student-t copulas are best at fitting the structure dependence between markets. Also, these copulas suggest that under normal market conditions, Bitcoin might act as a hedge asset against the stock price movements of all international markets analyzed. However, the dependence on the Shanghai and Hong Kong markets was somewhat higher. Also, under extreme market conditions, the role of Bitcoin might change from hedge to diversifier. In a time-varying copula analysis, given by the Student-t copula, we found that even under normal market conditions, for some markets, the role of Bitcoin as a hedge asset might fail on a high number of days.

Diverse Large HIV-1 Non-subtype B Clusters Are Spreading Among Men Who Have Sex With Men in Spain

In Western Europe, the HIV-1 epidemic among men who have sex with men (MSM) is dominated by subtype B. However, recently, other genetic forms have been reported to circulate in this population, as evidenced by their grouping in clusters predominantly comprising European individuals. Here we describe four large HIV-1 non-subtype B clusters spreading among MSM in Spain. Samples were collected in 9 regions. A pol fragment was amplified from plasma RNA or blood-extracted DNA. Phylogenetic analyses were performed via maximum likelihood, including database sequences of the same genetic forms as the identified clusters. Times and locations of the most recent common ancestors (MRCA) of clusters were estimated with a Bayesian method. Five large non-subtype B clusters associated with MSM were identified. The largest one, of F1 subtype, was reported previously. The other four were of CRF02_AG (CRF02_1; n = 115) and subtypes A1 (A1_1; n = 66), F1 (F1_3; n = 36), and C (C_7; n = 17). Most individuals belonging to them had been diagnosed of HIV-1 infection in the last 10 years. Each cluster comprised viruses from 3 to 8 Spanish regions and also comprised or was related to viruses from other countries: CRF02_1 comprised a Japanese subcluster and viruses from 8 other countries from Western Europe, Asia, and South America; A1_1 comprised viruses from Portugal, United Kingom, and United States, and was related to the A1 strain circulating in Greece, Albania and Cyprus; F1_3 was related to viruses from Romania; and C_7 comprised viruses from Portugal and was related to a virus from Mozambique. A subcluster within CRF02_1 was associated with heterosexual transmission. Near full-length genomes of each cluster were of uniform genetic form. Times of MRCAs of CRF02_1, A1_1, F1_3, and C_7 were estimated around 1986, 1989, 2013, and 1983, respectively. MRCA locations for CRF02_1 and A1_1 were uncertain (however initial expansions in Spain in Madrid and Vigo, respectively, were estimated) and were most probable in Bilbao, Spain, for F1_3 and Portugal for C_7. These results show that the HIV-1 epidemic among MSM in Spain is becoming increasingly diverse through the expansion of diverse non-subtype B clusters, comprising or related to viruses circulating in other countries.

Evaluation of the effect of polymorphism on G-quadruplex-ligand interaction by means of spectroscopic and chromatographic techniques

Guanine-rich sequences may fold into highly ordered structures known as G-quadruplexes. Apart from the monomeric G-quadruplex, these sequences may form multimeric structures that are not usually considered when studying interaction with ligands. This work studies the interaction of a ligand, crystal violet, with three guanine-rich DNA sequences with the capacity to form multimeric structures. These sequences correspond to short stretches found near the promoter regions of c-kit and SMARCA4 genes. Instrumental techniques (circular dichroism, molecular fluorescence, size-exclusion chromatography and electrospray ionization mass spectrometry) and multivariate data analysis were used for this purpose. The polymorphism of G-quadruplexes was characterized prior to the interaction studies. The ligand was shown to interact preferentially with the monomeric G-quadruplex; the binding stoichiometry was 1:1 and the binding constant was in the order of 10⁵M^-1 for all three sequences. The results highlight the importance of DNA treatment prior to interaction studies.

Abstract OT1-01-02: A multicenter phase II trial to evaluate the efficacy and safety of pembrolizumab and gemcitabine in patients with HER2-negative advanced breast cancer: GEICAM/2015-04 PANGEA-Breast

Background: Treatment options for advanced breast cancer (ABC) are multiple but unable to properly respond to current clinical needs. In particular, improved therapies are needed for triple negative and hormone receptor (HR)-positive but heavily pretreated patients. Pembrolizumab (P) is a human monoclonal antibody that blocks the PD-1/PD-L1 interaction hence potentiates anticancer T cell responses. Gemcitabine (G) is a cytotoxic drug with well-known immunostimulatory properties. Here, we report an ongoing phase II clinical trial to identify the Recommended Phase II Dose (RP2D) and the efficacy of the combination of these two agents in ABC patients. We hypothesize that these agents may synergize to induce responses with long term clinical benefit (ClinicalTrials.gov Identifier: NCT03025880).

Trial Design:

Eligible patients are HER2-negative ABC patients who received prior treatment with anthracyclines and taxanes and two or more prior lines of hormone therapy, if HR-positive disease. Patients with CNS involvement are also eligible if clinically stable. Treatment consists of 21-day cycles with 200 mg P on day 1 and G on days 1 and 8. In the safety dose testing, we use a standard 6+6 design with 2 dose levels (DL) of G: 1250 mg/m2 (DL0) and 1000 mg/m2 (DL1). Patients are treated until radiologic or symptomatic progression, or unacceptable toxicity. The primary objectives are RP2D and objective response rate (ORR) of the combination; secondary objectives include evaluation of safety and tolerability and other efficacy variables (progression-free survival [PFS], clinical benefit rate [CBR], response duration [RD] and overall survival [OS]). Efficacy is measured by RECIST 1.1. and irRECIST. Safety is measured using the National Cancer Institute Common Terminology Criteria for Adverse Events (NCI-CTCAE) 4.0. As exploratory objectives, immunological biomarkers are analyzed in tumor biopsies and blood samples and correlated with (1) clinical efficacy and (2) disease outcomes.Sequential tumor samples are collected at baseline, cycle 3 and at progression. Blood samples are drawn at baseline, cycle 3, and cycle 6, or at post-treatment visit (whatever occurs first). Tumor samples are characterized for intratumoral and stromal tumor-infiltrating lymphocytes, tumor-associated macrophages and myeloid-derived suppressor cells, PD-L1 expression in tumor cells and stroma. Moreover, molecular and genetic profiling will be performed. Blood samples are characterized for peripheral blood mononuclear cell (PBMC) phenotype (including expression of co-activatory and co-inhibitory receptors), cytokine profile, and activity of other immunosuppressive pathways (e.g., IDO1-dependent tryptophan catabolism). These results will be compared with data from a cohort of healthy volunteers.

A maximum of 65 patients will be included. The study is approved by the ethical committee and Competent Authority of Spain and already open for patient recruitment in 2 of the 10 participating sites.

Keywords:

Breast

HER2 negative

Pembrolizumab

Immunotherapy

Citation Format: de la Cruz L, Sánchez-Margalet V, Berraondo P, Benito S, Escudero MJ, Caballero R, Carrasco E, Galluzzi L, Rojo F. A multicenter phase II trial to evaluate the efficacy and safety of pembrolizumab and gemcitabine in patients with HER2-negative advanced breast cancer: GEICAM/2015-04 PANGEA-Breast [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr OT1-01-02.

Estimating Respiratory Pattern Variability by Symbolic Dynamics

Objectives: The traditional techniques of data analysis are often not sufficient to characterize the complex dynamics of respiration. In this study the respiratory pattern variability was analyzed using symbolic dynamics.

Methods: A group of 20 patients on weaning trials from mechanical ventilation were studied at two different pressure support ventilation levels. Breath duration (TTOT) time series and the relation TI/TTOT, that contains the influence of inspiratory time (TI), were considered. Length-3 words and 3 different symbols were proposed. The incidence of the overlapping τ and the parameter α were analyzed.

Results: From the breath duration time series, the distribution of words with probability of occurrence higher than 6% was concentrated on one word for low respiratory variability, whereas high variability was characterized by 4 words, presenting a statistically significant difference (p ≤ 0.0005). The probability occurrence of words “110” and “111” was also significantly different (p ≤ .0005) when comparing both variabilities.

Conclusion: The analysis carried out obtained discriminant functions able to correctly classify all the testing set series. These results permit the consideration of symbolic dynamics as a promising methodology to study the respiratory pattern variability.

Untargeted metabolomics for plasma biomarker discovery for early chronic kidney disease diagnosis in pediatric patients using LC-QTOF-MS

Pediatric chronic kidney disease (CKD) is a clinical syndrome characterized by renal hypofunction occurring due to gradual and irreversible kidney damage that can further progress over time.

Plasma biomarker discovery for early chronic kidney disease diagnosis based on chemometric approaches using LC-QTOF targeted metabolomics data

Chronic kidney disease (CKD) is a progressive pathological condition in which renal function deteriorates in time. The first diagnosis of CKD is often carried out in general care attention by general practitioners by means of serum creatinine (CNN) levels. However, it lacks sensitivity and thus, there is a need for new robust biomarkers to allow the detection of kidney damage particularly in early stages. Multivariate data analysis of plasma concentrations obtained from LC-QTOF targeted metabolomics method may reveal metabolites suspicious of being either up-regulated or down-regulated from urea cycle, arginine methylation and arginine-creatine metabolic pathways in CKD pediatrics and controls. The results show that citrulline (CIT), symmetric dimethylarginine (SDMA) and S-adenosylmethionine (SAM) are interesting biomarkers to support diagnosis by CNN: early CKD samples and controls were classified with an increase in classification accuracy of 18% when using these 4 metabolites compared to CNN alone. These metabolites together allow classification of the samples into a definite stage of the disease with an accuracy of 74%, being the 90% of the misclassifications one level above or below the CKD stage set by the nephrologists. Finally, sex-related, age-related and treatment-related effects were studied, to evaluate whether changes in metabolite concentration could be attributable to these factors, and to correct them in case a new equation is developed with these potential biomarkers for the diagnosis and monitoring of pediatric CKD.

Abstract OT3-01-02: A phase I-II trial of dasatinib in combination with trastuzumab (T) and paclitaxel in the first line treatment of HER2 positive metastatic breast cancer (MBC) patients: GEICAM/2010-04

Background: Resistance to targeted-therapies is a current problem in our clinical practice. In HER2 overexpressing tumors, resistance to trastuzumab-based therapies is widely observed. Expression of SRC has been pre-clinically linked to trastuzumab resistance and the addition of the multi-tyrosine kinase inhibitor dasatinib to trastuzumab increases its antitumor activity (Seoane S, et al. J Natl Cancer Inst. 2010). On previous studies, Dasatinib showed a good toxicity profile, with low grade 3-4 toxicity rates (E. Mayer, et al. J Clin Oncol 2009). We have designed a phase I-II trial combining dasatinib with standard trastuzumab/paclitaxel. (ClinicalTrials.gov Identifier: NCT01306942). In this abstract we report the description of the phase II part of the trial which is ongoing.

Trial Design: Eligible patients must be HER2+ (evaluated by central laboratory and assessed by immunohistochemistry and fluorescent in-situ hybridization) MBC and candidates for trastuzumab + chemotherapy as first line treatment. Taxanes and trastuzumab administered in the adjuvant setting are permitted if given &gt;12 months before the inclusion. Patients with CNS involvement are eligible if treated and clinically stable without medication. Treatment consists of trastuzumab 2 mg/kg weekly (following a loading dose of 4 mg/kg in cycle 1), weekly paclitaxel (80 mg/m2, 3 weeks on-one week off) and dasatinib 100 mg once daily (based on the recommended phase II dose from the phase I part, Gil-Martin M, et al. European Breast Cancer Conference 2014, P-041) in a 28-days cycle. Patients are treated until radiologic or symptomatic progression or unacceptable toxicity.

The primary objective for this phase II is efficacy, measured by Objective Response Rate (ORR according to RECIST 1.1). Secondary objectives are: Safety (evaluated using NCI-CTCAE v 4.03), Clinical Benefit Rate, Time to Progression, Progression Free Survival and Response Duration. Pharmacodynamic biomarkers include pAKT, pS6, pSRC, pErk1/2 in tumor tissue samples, mononuclear cells in blood samples and in skin tissue. An additional exploratory objective is to evaluate the correlation between the early presence of lymphocytosis and efficacy. The study will be considered positive if ORR increases 25% from a 50% ORR observed in previous studies with paclitaxel + trastuzumab. We need to include 28 evaluable patients to demonstrate this hypothesis (with an alpha error of 0.05 and a statistical power of 80%), assuming a 10% drop-out rate. Twenty one patients have already been included. Recruitment is expected to finish by the end of 2015.

Citation Format: Ocaña A, Ruiz Borrego M, Gil-Martín M, Antolín S, Guerrero Á, Vidal Boixader L, Martín M, Trigo Pérez JM, Rojo F, Jerez Y, Atienza M, Pernas S, Hernando A, Carrasco E, Benito S, Caballero R, Pandiella A. A phase I-II trial of dasatinib in combination with trastuzumab (T) and paclitaxel in the first line treatment of HER2 positive metastatic breast cancer (MBC) patients: GEICAM/2010-04. [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 OT3-01-02.

Classification of patients undergoing weaning from mechanical ventilation using the coherence between heart rate variability and respiratory flow signal

Weaning from mechanical ventilation is still one of the most challenging problems in intensive care. Unnecessary delays in discontinuation and weaning trials that are undertaken too early are both undesirable. This study investigated the contribution of spectral signals of heart rate variability (HRV) and respiratory flow, and their coherence to classifying patients on weaning process from mechanical ventilation. A total of 121 candidates for weaning, undergoing spontaneous breathing tests, were analyzed: 73 were successfully weaned (GSucc), 33 failed to maintain spontaneous breathing so were reconnected (GFail), and 15 were extubated after the test but reintubated within 48 h (GRein). The power spectral density and magnitude squared coherence (MSC) of HRV and respiratory flow signals were estimated. Dimensionality reduction was performed using principal component analysis (PCA) and sequential floating feature selection. The patients were classified using a fuzzy K-nearest neighbour method. PCA of the MSC gave the best classification with the highest accuracy of 92% classifying GSucc versus GFail patients, and 86% classifying GSucc versus GRein patients. PCA of the respiratory flow signal gave the best classification between GFail and GRein patients (79% accuracy). These classifiers showed a good balance between sensitivity and specificity. Besides, the spectral coherence between HRV and the respiratory flow signal, in patients on weaning trial process, can contribute to the extubation decision.

Exploring the antigenic relatedness of influenza virus haemagglutinins with strain-specific polyclonal antibodies

Alternative methods to the standard haemagglutination inhibition (HI) and neutralization tests to probe the antigenic properties of the influenza virus haemagglutinin (HA) were developed in this study. Vaccinia virus recombinants expressing reference HAs were used to immunize rabbits from which polyclonal antibodies were obtained. These antibodies were subtype specific but showed limited intra-subtype strain specificity in ELISA. The discriminatory capacity of these antibodies was, however, markedly increased after adsorption to cells infected with heterologous influenza viruses, revealing antigenic differences that were otherwise undistinguishable by standard HI and neutralization tests. Furthermore, the unadsorbed antibodies could be used to select escape mutants of the reference strain, which after sequencing unveiled amino acid changes responsible of the noted antigenic differences. These procedures therefore provide alternative methods for the antigenic characterization of influenza HA and might be useful in studies of HA antigenic evolution.

Characterization of an enhanced antigenic change in the pandemic 2009 H1N1 influenza virus haemagglutinin

Murine hybridomas producing neutralizing mAbs specific to the pandemic influenza virus A/California/07/2009 haemagglutinin (HA) were isolated. These antibodies recognized at least two different but overlapping new epitopes that were conserved in the HA of most Spanish pandemic isolates. However, one of these isolates (A/Extremadura/RR6530/2010) lacked reactivity with the mAbs and carried two unique mutations in the HA head (S88Y and K136N) that were required simultaneously to eliminate reactivity with the murine antibodies. This unusual requirement directly illustrates the phenomenon of enhanced antigenic change proposed previously for the accumulation of simultaneous amino acid substitutions at antigenic sites of the influenza A virus HA during virus evolution (Shih et al., Proc Natl Acad Sci USA, 104 , 6283-6288, 2007). The changes found in the A/Extremadura/RR6530/2010 HA were not found in escape mutants selected in vitro with one of the mAbs, which contained instead nearby single amino acid changes in the HA head. Thus, either single or double point mutations may similarly alter epitopes of the new antigenic site identified in this work in the 2009 H1N1 pandemic virus HA. Moreover, this site is relevant for the human antibody response, as shown by competition of mAbs and human post-infection sera for virus binding. The results are discussed in the context of the HA antigenic structure and challenges posed for identification of sequence changes with possible antigenic impact during virus surveillance.

Reduction of 4-ethylphenol production in red wines using HCDC+ yeasts and cinnamyl esterases

Hydroxycinnamate decarboxylase (HCDC) activity has been evaluated in several commercial yeast strains. The combined effect of using cinnamyl esterases (CE) and HCDC+ Saccharomyces cerevisiae strains has been studied in the formation of vinylphenolic pyranoanthocyanins (VPAs) during fermentation, analysing the kind and concentration of pigments formed according to the yeast strain used. Wines fermented with yeasts HCDC+ were contaminated with Dekkera bruxellensis and afterwards analysed to evaluate the formation of ethylphenols (EPs). The musts treated with CE and later fermented with HCDC+ yeast strains showed lower contents of 4-ethylphenol than those fermented with HCDC- strains. This reduction in the EP content is due to the transformation of hydroxycinnamic acids in stable VPAs pigments. The associated use of CEs and HCDC+ Saccharomyces strains is a natural strategy to reduce the formation of EPs in wines contaminated by Dekkera/Brettanomyces.

Formation of pyranoanthocyanins by Schizosaccharomyces pombe during the fermentation of red must

Schizosaccharomyces pombe is a non-Saccharomyces yeast strain that can ferment grape musts with high sugar contents - but it also has other metabolic and physiological properties that render it of great interest to wine biotechnologists. This work compares the production of pyranoanthocyanins by S. pombe, Saccharomyces cerevisiae and Saccharomyces uvarum during fermentation. Total pyranoanthocyanins ranged from 11.9 to 19.4 mg/l depending on the strain of S. pombe used. On average, S. pombe produced more pyruvic acid than did either Saccharomyces species; as a consequence it also formed more vitisin A-type pigments. S. pombe 938 produced the largest quantity of vitisin A (11.03±0.82 mg/l). The formation of large amounts of pyranoanthocyanins intensifies the post-fermentation colour of wines somewhat, a phenomenon that helps them maintain their colour over ageing as the natural grape anthocyanins become degraded. Some of the S. pombe strains showed hydroxycinnamate decarboxylase activity, which favours the formation of vinylphenolic pyranoanthocyanins. Fermentation with S. pombe therefore provides an interesting way of increasing the overall pyranoanthocyanin content of red wines, and of stabilising their colour during ageing.

Mediterranean diet and the incidence of cardiovascular disease: a Spanish cohort

BACKGROUND AND AIM

The Mediterranean diet is considered a model for healthy eating. However, prospective evidence in Mediterranean countries evaluating the relationship between this dietary pattern and non-fatal cardiovascular events is scarce. The aim of the present study was to evaluate the association between the adherence to the Mediterranean diet and the incidence of fatal and non-fatal cardiovascular events among initially healthy middle-aged adults from the Mediterranean area.

METHODS AND RESULTS

We followed-up 13,609 participants (60 percent women, mean age: 38 years) initially free of cardiovascular disease (CVD) during 4.9 years. Participants were part of a prospective cohort study of university graduates from all regions of Spain. Baseline diet was assessed using a validated 136-item food-frequency questionnaire. A 9-point score was used to appraise adherence to the Mediterranean diet. Incident clinical events were confirmed by a review of medical records. We observed 100 incident cases of CVD. In multivariate analyses, participants with the highest adherence to the Mediterranean diet (score>6) exhibited a lower cardiovascular risk (hazard ratio=0.41, 95% confidence interval [CI]: 0.18-0.95) compared to those with the lowest score (<3). For each 2-point increment in the score, the adjusted hazard ratios were 0.80 (95% CI: 0.62-1.02) for total CVD and 0.74 (0.55-0.99) for coronary heart disease.

CONCLUSIONS

There is an inverse association between adherence to the Mediterranean diet and the incidence of fatal and non-fatal CVD in initially healthy middle-aged adults.

Symbolic dynamic analysis of relations between cardiac and breathing cycles in patients on weaning trials

Traditional time-domain techniques of data analysis are often not sufficient to characterize the complex dynamics of the cardiorespiratory interdependencies during the weaning trials. In this paper, the interactions between the heart rate (HR) and the breathing rate (BR) were studied using joint symbolic dynamic analysis. A total of 133 patients on weaning trials from mechanical ventilation were analyzed: 94 patients with successful weaning (group S) and 39 patients that failed to maintain spontaneous breathing (group F). The word distribution matrix enabled a coarse-grained quantitative assessment of short-term nonlinear analysis of the cardiorespiratory interactions. The histogram of the occurrence probability of the cardiorespiratory words presented a higher homogeneity in group F than in group S, measured with a higher number of forbidden words in group S as well as a higher number of words whose probability of occurrence is higher than a probability threshold in group S. The discriminant analysis revealed the best results when applying symbolic dynamic variables. Therefore, we hypothesize that joint symbolic dynamic analysis provides enhanced information about different interactions between HR and BR, when comparing patients with successful weaning and patients that failed to maintain spontaneous breathing in the weaning procedure.

A method for estimating Dekkera/Brettanomyces populations in wines

AIMS

The formation of ethylphenols in wines, a consequence of Dekkera/Brettanomyces metabolism, can affect their quality. The main aims of this work were to further our knowledge of Dekkera/Brettanomyces with respect to ethylphenol production, and to develop a methodology for detecting this spoilage yeast and for estimating its population size in wines using differential-selective media and high performance liquid chromatography (HPLC).

METHODS AND RESULTS

This work examines the reduction of p-coumaric acid and the formation of 4-vinylphenol and 4-ethylphenol (recorded by HPLC-DAD) in a prepared medium because of the activities of different yeast species and populations. A regression model was constructed for estimating the population of Dekkera/Brettanomyces at the beginning of fermentation via the conversion of hydroxycinnamic acids into ethylphenols.

CONCLUSIONS

The proposed methodology allows the populations of Dekkera/Brettanomyces at the beginning of fermentation to be estimated in problem wines. Moreover, it avoids false positives because of yeasts resistant to the effects of the selective elements of the medium.

SIGNIFICANCE AND IMPACT OF THE STUDY

This may help prevent the appearance of organoleptic anomalies in wines at the winery level.

Adherence to Mediterranean diet and risk of developing diabetes: prospective cohort study

OBJECTIVE

To assess the relation between adherence to a Mediterranean diet and the incidence of diabetes among initially healthy participants.

DESIGN

Prospective cohort study with estimates of relative risk adjusted for sex, age, years of university education, total energy intake, body mass index, physical activity, sedentary habits, smoking, family history of diabetes, and personal history of hypertension.

SETTING

Spanish university department.

PARTICIPANTS

13 380 Spanish university graduates without diabetes at baseline followed up for a median of 4.4 years.

MAIN OUTCOME MEASURES

Dietary habits assessed at baseline with a validated 136 item food frequency questionnaire and scored on a nine point index. New cases of diabetes confirmed through medical reports and an additional detailed questionnaire posted to those who self reported a new diagnosis of diabetes by a doctor during follow-up. Confirmed cases of type 2 diabetes.

RESULTS

Participants who adhered closely to a Mediterranean diet had a lower risk of diabetes. The incidence rate ratios adjusted for sex and age were 0.41 (95% confidence interval 0.19 to 0.87) for those with moderate adherence (score 3-6) and 0.17 (0.04 to 0.75) for those with the highest adherence (score 7-9) compared with those with low adherence (score <3). In the fully adjusted analyses the results were similar. A two point increase in the score was associated with a 35% relative reduction in the risk of diabetes (incidence rate ratio 0.65, 0.44 to 0.95), with a significant inverse linear trend (P=0.04) in the multivariate analysis.

CONCLUSION

Adherence to a Mediterranean diet is associated with a reduced risk of diabetes.

Adherence to Mediterranean diet and risk of developing diabetes: prospective cohort study

OBJECTIVE

To assess the relation between adherence to a Mediterranean diet and the incidence of diabetes among initially healthy participants.

DESIGN

Prospective cohort study with estimates of relative risk adjusted for sex, age, years of university education, total energy intake, body mass index, physical activity, sedentary habits, smoking, family history of diabetes, and personal history of hypertension.

SETTING

Spanish university department.

PARTICIPANTS

13 380 Spanish university graduates without diabetes at baseline followed up for a median of 4.4 years.

MAIN OUTCOME MEASURES

Dietary habits assessed at baseline with a validated 136 item food frequency questionnaire and scored on a nine point index. New cases of diabetes confirmed through medical reports and an additional detailed questionnaire posted to those who self reported a new diagnosis of diabetes by a doctor during follow-up. Confirmed cases of type 2 diabetes.

RESULTS

Participants who adhered closely to a Mediterranean diet had a lower risk of diabetes. The incidence rate ratios adjusted for sex and age were 0.41 (95% confidence interval 0.19 to 0.87) for those with moderate adherence (score 3-6) and 0.17 (0.04 to 0.75) for those with the highest adherence (score 7-9) compared with those with low adherence (score <3). In the fully adjusted analyses the results were similar. A two point increase in the score was associated with a 35% relative reduction in the risk of diabetes (incidence rate ratio 0.65, 0.44 to 0.95), with a significant inverse linear trend (P=0.04) in the multivariate analysis.

CONCLUSION

Adherence to a Mediterranean diet is associated with a reduced risk of diabetes.

Information flow to assess cardiorespiratory interactions in patients on weaning trials

Nonlinear processes of the autonomic nervous system (ANS) can produce breath-to-breath variability in the pattern of breathing. In order to provide assess to these nonlinear processes, nonlinear statistical dependencies between heart rate variability and respiratory pattern variability are analyzed. In this way, auto-mutual information and cross-mutual information concepts are applied. This information flow analysis is presented as a short-term non linear analysis method to investigate the information flow interactions in patients on weaning trials. 78 patients from mechanical ventilation were studied: Group A of 28 patients that failed to maintain spontaneous breathing and were reconnected; Group B of 50 patients with successful trials. The results show lower complexity with an increase of information flow in group A than in group B. Furthermore, a more (weakly) coupled nonlinear oscillator behavior is observed in the series of group A than in B.