Marília Antunes

A preliminary algorithm introducing immunogenicity assessment in the management of patients with RA receiving tumour necrosis factor inhibitor therapies

Introduction Clinical remission is today the treatment goal for rheumatoid arthritis (RA), which requires fast and assertive therapeutic decisions for a tight control of disease activity. Few objective parameters are available to guide clinical decisions, particularly in switcher patients. We designed a preliminary algorithm introducing immunogenicity assessment in the current approach to patients with RA receiving tumour necrosis factor inhibitors (TNFi). Objective To evaluate the concordance between the new algorithm and current clinical practice, comparing the effectiveness of ‘immunogenicity-based’ versus ‘empirical-based’ switches in a cohort of patients with established RA receiving biologics. Methods EULAR therapeutic response was evaluated in 105 patients with RA (naive or switchers) over one year, through generalised estimation equation (GEE) analyses. Serum drug trough levels were assessed by ELISA and antidrug antibodies (ADAb) by Bridging ELISA. Results During follow-up, 48.6% of patients had therapeutic decisions concordant with the proposed algorithm (Group A), and 51.4% had discordant decisions (Group B). One year after the therapeutic decision, patients from Group A had a higher probability of achieving response (OR=7.91, p<0.001, 95% CI 3.27 to 19.13) and low disease activity (OR=9.77, p<0.001, 95% CI 4.69 to 20.37) than patients in Group B. Conclusions Immunogenicity assessment might help to optimise therapeutic decisions, leading to a better control of disease activity with significantly better clinical outcomes in patients with RA receiving TNFi.

Contribution for new genetic markers of rheumatoid arthritis activity and severity: sequencing of the tumor necrosis factor-alpha gene promoter

The objective of this study was to assess whether clinical measures of rheumatoid arthritis activity and severity were influenced by tumor necrosis factor-alpha (TNF-α) promoter genotype/haplotype markers. Each patients disease activity was assessed by the disease activity score using 28 joint counts (DAS28) and functional capacity by the Health Assessment Questionnaire (HAQ) score. Systemic manifestations, radiological damage evaluated by the Sharp/van der Heijde (SvdH) score, disease-modifying anti-rheumatic drug use, joint surgeries, and work disability were also assessed. The promoter region of the TNF-α gene, between nucleotides -1,318 and +49, was sequenced using an automated platform. Five hundred fifty-four patients were evaluated and genotyped for 10 single-nucleotide polymorphism (SNP) markers, but 5 of these markers were excluded due to failure to fall within Hardy-Weinberg equilibrium or to monomorphism. Patients with more than 10 years of disease duration (DD) presented significant associations between the -857 SNP and systemic manifestations, as well as joint surgeries. Associations were also found between the -308 SNP and work disability in patients with more than 2 years of DD and radiological damage in patients with less than 10 years of DD. A borderline effect was found between the -238 SNP and HAQ score and radiological damage in patients with 2 to 10 years of DD. An association was also found between haplotypes and the SvdH score for those with more than 10 years of DD. An association was found between some TNF-α promoter SNPs and systemic manifestations, radiological progression, HAQ score, work disability, and joint surgeries, particularly in some classes of DD and between haplotypes and radiological progression for those with more than 10 years of DD.

DFNB1-associated deafness in Portuguese cochlear implant users: prevalence and impact on oral outcome.

OBJECTIVES Hearing loss is a condition that interferes with the development of the child at a cognitive and language level. Therefore, early diagnosis of deafness is important for (re)habilitation, namely through the use of cochlear implant (CI). The present study aimed at screening CI Portuguese individuals for the presence of mutations in the genes GJB2 and GJB6 (DFNB1 locus), and searching a possible correlation between the genotype and the oral habilitation outcome following implantation. METHODS Our sample included 117 CI individuals implanted longer than 5 years. Sequencing of GJB2 entire coding region was first performed. The presence of deletions del(GJB6-D13S1830) and del(GJB6-D13S1854) was subsequently tested by multiplex PCR. To assess the oral outcome of these individuals, a global score is calculated through a formula that integrates the results of a battery of speech and audiological tests routinely used in ORL services. This global oral performance score was used to test whether individuals with DFNB1-associated deafness perform significantly better than individuals without DFNB1-associated deafness. RESULTS In 35% of the cases, deafness was clearly associated to DFNB1. The most common mutated allele was c.35delG (85%). Other variants have also been found, namely p.Gly130Ala, p.Asn206Ser, p.Val37Ile, p.Glu47X, p.Arg184Trp, p.Trp24X and the two common GJB6 deletions, del(GJB6-D13S1854) and del(GJB6-D13S1830), the last one identified for the first time in our population. Regarding the oral outcome, after testing the homogeneity of the two groups it could be observed that, in mean, the individuals with DFNB1-associated deafness perform significantly better (p=0.012) than the individuals without DFNB1-associated deafness. DISCUSSION AND CONCLUSION This first screening of DFNB1 genes in the Portuguese CI population provides clear evidence of the high proportion of DFNB1-associated deafness amongst the Portuguese implanted individuals. DFNB1 status is significantly associated to higher oral performance scores, with DFNB1 individuals performing, on average, 6% better than the individuals without DFNB1-associated deafness.

Healthcare recommendations from the Personalised ICT Supported Service for Independent Living and Active Ageing (PERSSILAA) Study

In the face of demographic ageing European healthcare providers and policy makers are recognising an increasing prevalence of frail, community-dwelling older adults, prone to adverse healthcare outcomes. Prefrailty, before onset of functional decline, is suggested to be reversible but interventions targeting this risk syndrome are limited. No consensus on the definition, diagnosis or management of pre-frailty exists. The PERsonalised ICT Supported Service for Independent Living and Active Ageing (PERSSILAA) project (2013-2016 under Framework Programme 7, grant #610359) developed a comprehensive Information and Communication Technologies (ICT) supported platform to screen, assess, manage and monitor pre-frail community-dwelling older adults in order to address pre-frailty and promote active and healthy ageing. PERSSILAA, a multi-domain ICT service, targets three pre-frailty: nutrition, cognition and physical function. The project produced 42 recommendations across clinical (screening, monitoring and managing of pre-frail older adults) technical (ICT-based innovations) and societal (health literacy in older adults, guidance to healthcare professional, patients, caregivers and policy makers) areas. This paper describes the 25 healthcare related recommendations of PERSSILAA, exploring how they could be used in the development of future European guidelines on the screening and prevention of frailty.

Bayesian classification for bivariate normal gene expression

A Bayesian optimal screening method (BOSc) is proposed to classify an individual into one of two groups, based on the observation of pairs of covariates, namely the expression level of pairs of genes (previously selected by a specific method, among the thousands of genes present in the microarray) measured using DNA microarrays technology. The method is general and can be applied to any correlated pair of screening variables, either with a bivariate normal distribution or which can be transformed into a bivariate normal. Results on microarray data sets (Leukemia, Prostate and Breast) show that BOSc performance is competitive with, and in some cases significantly better than, quadratic and linear discriminant analyses and support vector machines classifiers. BOSc provides flexible parametric decision rules. Finally, the screening classifier allows the calculation of operating characteristics while addressing information about the prevalence of the disease or type of disease, which is an advantage over other classification methods.

Bayesian classification and non-Bayesian label estimation via EM algorithm to identify differentially expressed genes: a comparative study.

Gene classification problem is studied considering the ratio of gene expression levels, X, in two-channel microarrays and a non-observed categorical variable indicating how differentially expressed the gene is: non differentially expressed, down-regulated or up-regulated. Supposing X from a mixture of Gamma distributions, two methods are proposed and results are compared. The first method is based on an hierarchical Bayesian model. The conditional predictive probability of a gene to belong to each group is calculated and the gene is assigned to the group for which this conditional probability is higher. The second method uses EM algorithm to estimate the most likely group label for each gene, that is, to assign the gene to the group which contains it with the higher estimated probability.

ICT-Supported Interventions Targeting Pre-frailty: Healthcare Recommendations from the Personalised ICT Supported Service for Independent Living and Active Ageing (PERSSILAA) Study

As society ages, healthcare systems are preparing for an increasing prevalence of frail, co-morbid and older community-dwellers at risk of adverse outcomes including falls, malnutrition, hospitalisation, institutionalisation and death. Early intervention is desirable and pre-frailty, before onset of functional decline, may represent a suitable transition stage to target, albeit evidence for reversibility and appropriate interventions are limited. No consensus on the definition, diagnosis or management of pre-frailty exists. This work describes 25 healthcare related findings from the recently completed PERsonalised ICT Supported Service for Independent Living and Active Ageing (PERSSILAA) project, funded under the 2013–2016 European Union Framework Programme 7 (grant #610359). PERSSILAA developed a comprehensive Information and Communication Technologies (ICT)-supported platform to screen, assess, intervene and then monitor community-dwellers in two regions (Enschede in the Netherlands and Campania in Italy) in order to address pre-frailty and promote active and healthy ageing, targeting three important pre-frailty subdomains: nutrition, cognition and physical function. Proposed definitions of pre-frailty, ICT-based approaches to screen and monitor for the onset of frailty and targeted management strategies employing technology across these domains are described. The potential of these 25 healthcare recommendations in the development of future European guidelines on the screening and prevention of frailty is explored.

Biomarkers of presbycusis and tinnitus in a Portuguese older population

Introduction: Presbycusis or age-related hearing loss (ARHL) is a ubiquitous health problem. It is estimated that it will affect up to 1.5 billion people by 2025. In addition, tinnitus occurs in a large majority of cases with presbycusis. Glutamate metabotropic receptor 7 (GRM7) and N-acetyltransferase 2 (NAT2) are some of the genetic markers for presbycusis. Objectives: To explore patterns of hearing loss and the role of GRM7 and NAT2 as possible markers of presbycusis and tinnitus in a Portuguese population sample. Materials and Methods: Tonal and speech audiometry, tinnitus assessment, clinical interview, and DNA samples were obtained from patients aged from 55 to 75 with or without tinnitus. GRM7 analysis was performed by qPCR. Genotyping of single nucleotide polymorphisms (SNPs) in NAT2 was performed by PCR amplification followed by Sanger sequencing or by qPCR. Results: We screened samples from 78 individuals (33 men and 45 women). T allele at GRM7 gene was the most observed (60.3% T/T and 33.3% A/T). Individuals with a T/T genotype have a higher risk for ARHL and 33% lower risk for tinnitus, compared to individuals with A/A and A/T genotype, respectively. Being a slow acetylator (53%) was the most common NAT2 phenotype, more common in men (55.8%). Intermediate acetylator was the second most common phenotype (35.9%) also more frequent in men (82.6%). Noise exposed individuals and individuals with ‘high frequency’ hearing loss seem to have a higher risk for tinnitus. Our data suggests that allele AT of GRM7 can have a statistically significant influence toward the severity of tinnitus. Conclusion: For each increasing year of age the chance of HL increases by 9%. The risk for ARHL was not significantly associated with GRM7 neither NAT2. However, we cannot conclude from our data whether the presence of T allele at GRM7 increases the odds for ARHL or whether the A allele has a protective effect. Genotype A/T at GRM7 could potentially be considered a biomarker of tinnitus severity. This is the first study evaluating the effect of GRM7 and NAT2 gene in tinnitus.

Determinants of Health Care Utilization in Hypertensive Patients: A Longitudinal Analysis.

The count variable number of GP visits (in the previous 3 months) had a large proportion of zeros, as some patients did not visit the doctor within this period. The average number of visits ranged between 0.43 (variance=0.54) at 3 months and 0.11 (variance=0.13) at 12 months. The results of the model indicate that higher income had a negative impact on the number of visits to GP for reasons related to hypertension, probably because people with higher income use private sector more often. Domestic work had a positive impact. Health variables, such as diabetes and number of medicines, which probably reflect a higher need, had a positive impact on GP visits. As expected, those who self-assessed their hypertension as controlled went fewer times to the GP (Table 2).

Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays.

BackgroundMicroarray-based comparative genomic hybridization (aCGH) is used for rapid comparison of genomes of different bacterial strains. The purpose is to evaluate the distribution of genes from sequenced bacterial strains (control) among unsequenced strains (test). We previously compared the use of single strain versus multiple strain control with arrays covering multiple genomes. The conclusion was that a multiple strain control promoted a better separation of signals between present and absent genes.FindingsWe now extend our previous study by applying the Expectation-Maximization (EM) algorithm to fit a mixture model to the signal distribution in order to classify each gene as present or absent and by comparing different methods for analyzing aCGH data, using combinations of different control strain choices, two different statistical mixture models, with or without normalization, with or without logarithm transformation and with test-over-control or inverse signal ratio calculation. We also assessed the impact of replication on classification accuracy. Higher values of accuracy have been achieved using the ratio of control-over-test intensities, without logarithmic transformation and with a strain mix control. Normalization and the type of mixture model fitted by the EM algorithm did not have a significant impact on classification accuracy. Similarly, using the average of replicate arrays to perform the classification does not significantly improve the results.ConclusionsOur work provides a guiding benchmark comparison of alternative methods to analyze aCGH results that can impact on the analysis of currently ongoing comparative genomic projects or in the re-analysis of published studies.