Portuguese consensus document for the management of alpha-1-antitrypsin deficiency

Alpha-1-antitrypsin deficiency (AATD) is a genetic autosomal codominant disorder caused by mutations in SERPINA1 gene. It is one of the most prevalent genetic disorders, although it remains underdiagnosed. Whereas at international level there are several areas of consensus on this disorder, in Portugal, inter-hospital heterogeneity in clinical practice and resources available have been adding difficulties in reaching a diagnosis and in making therapeutic decisions in this group of patients. This raised a need to draft a document expressing a national consensus for AATD. To this end, a group of experts in this field was created within the Portuguese Pulmonology Society - Study group on AATD, in order to elaborate the current manuscript. The authors reviewed the existing literature and provide here general guidance and extensive recommendations for the diagnosis and management of AATD that can be adopted by Portuguese clinicians from different areas of Medicine. This article is part of a supplement entitled "Portuguese consensus document for the management of alpha-1-antitrypsin deficiency" which is sponsored by Sociedade Portuguesa de Pneumologia.

Genes from the TAS1R and TAS2R Families of Taste Receptors: Looking for Signatures of Their Adaptive Role in Human Evolution

Taste perception is crucial in monitoring food intake and, hence, is thought to play a significant role in human evolution. To gain insights into possible adaptive signatures in genes encoding bitter, sweet, and umami taste receptors, we surveyed the available sequence variation data from the 1000 Genomes Project Phase 3 for TAS1R (TAS1R1-3) and TAS2R (TAS2R16 and TAS2R38) families. Our study demonstrated that genes from these two families have experienced contrasting evolutionary histories: While TAS1R1 and TAS1R3 showed worldwide evidence of positive selection, probably correlated with improved umami and sweet perception, the patterns of variation displayed by TAS2R16 and TAS2R38 were more consistent with scenarios of balancing selection that possibly conferred a heterozygous advantage associated with better capacity to perceive a wide range of bitter compounds. In TAS2R16, such adaptive events appear to have occurred restrictively in mainland Africa, whereas the strongest evidence in TAS2R38 was detected in Europe. Despite plausible associations between taste perception and the TAS1R and TAS2R selective signatures, we cannot discount other biological mechanisms as driving the evolutionary trajectories of those TAS1R and TAS2R members, especially given recent findings of taste receptors behaving as the products of pleiotropic genes involved in many functions outside the gustatory system.

Cytomegalic hepatitis in a patient receiving omalizumab

Cytomegalovirus is a double stranded DNA virus that can be present in nearly all organs and body fluids. The primary infection is usually asymptomatic in the immunocompetent host and it is common among adolescents and young adults. The symptomatic form appears, in the majority of cases, as a mononucleosis syndrome with full recovery without specific treatment. We report a case of a 25 years old woman who presented with hepatitis due to CMV infection and history of omalizumab administration one month earlier. This recombinant monoclonal antibody is used to control refractory asthma and chronic spontaneous urticarial as it inhibits human IgE. Despite that, the long course of the disease lead us to initiate treatment with valganciclovir. The improvement after that was rapid and complete.

Mucins MUC16 and MUC1 are major carriers of SLe(a) and SLe(x) in borderline and malignant serous ovarian tumors

Mucins are heavily glycosylated proteins overexpressed and associated with truncated or sialylated glycans upon malignant transformation. We previously identified a panel of four glyco-mucin profiles (MUC16/Tn, MUC16/STn, MUC1/Tn, and MUC1/STn) with 100 % specificity and 100 % positive predictive value for detection of borderline/malignant serous tumors of the ovary, using proximity ligation assay (PLA). In the present work, using the same method, we studied other mucin glycosylation profiles that might add relevant information for diagnostic purposes. We used PLA probes to MUC16, MUC1, sialyl Lewis(a) (SLe(a)), and sialyl Lewis(x) (SLe(x)) to study a series of 39 ovarian serous tumors (14 adenocarcinomas, 10 borderline ovarian tumors (BOTs), and 15 cystadenomas). Our results demonstrated that, in adenocarcinomas and BOTs, the major carriers of SLe(a) and SLe(x) are MUC16 and/or MUC1 (100 and 92 % for SLe(a) and 64 and 70 % for SLe(x), respectively). In cystadenomas, SLe(a) and SLe(x) are mainly carried by unidentified proteins (85 and 78 %, respectively). Our study identified, for the first time, the major protein carriers of SLe(a) and SLe(x) in ovarian adenocarcinomas and BOTs, MUC1 and MUC16, and also that distinct unidentified carriers are involved in cystadenomas. These results emphasize the relevance of multiple biomarker recognition provided by multiplex assays, such as PLA, to enhance sensitivity and specificity of serum and tissue assays.

Frequency of Pancreatic Hyperamylasemia in Human Immunodeficiency Virus-Positive Patients in the Highly Active Antiretroviral Therapy Era

OBJECTIVES

Increased frequency of hyperamylasemia has previously been reported in human immunodeficiency virus (HIV)-positive patients, but studies determined total amylase activity and were performed before the introduction of highly active antiretroviral therapy (HAART). We evaluated the frequency of pancreatic hyperamylasemia in a large HIV+ population mostly treated with HAART.

METHODS

The upper reference limit (URL) for pancreatic amylase (P-AMY) was derived from 299 healthy blood donors. A cross-sectional study was then performed on samples obtained from 1,548 consecutive patients referred to our infectious disease clinic to assess serum P-AMY and lipase concentrations. Of the patients, 94% were HIV+, and most (92%) were taking HAART (HIV+Tx+).

RESULTS

P-AMY URL was 51 U/L. The frequency of P-AMY increase did not significantly differ between HIV+ and HIV - populations (14.2% vs 15.2%, P = .91) or between HIV+Tx+ and HIV+Tx - (14.7% vs 8.9%, P = .11). In almost half (48.3% of HIV+ and 42.9% of HIV -) of hyperamylasemic patients, lipase was normal, indicating a non pancreatic origin of their P-AMY increase. Markedly elevated P-AMY (>3 times the URL) was found in six HIV+ patients and in one HIV - patient: two had macroamylasemia, one acute pancreatitis, three (including the HIV - patient) chronic pancreatitis, and one chronic hyperamylasemia of undefined origin.

CONCLUSIONS

In our study, both HIV+ and HIV+Tx+ do not show an increased frequency of P-AMY elevation. Frank pancreatic disease is rare in this clinical setting.

Exploring the relationship between lifestyles, diets and genetic adaptations in humans

Background

One of the most important dietary shifts underwent by human populations began to occur in the Neolithic, during which new modes of subsistence emerged and new nutrients were introduced in diets. This change might have worked as a selective pressure over the metabolic pathways involved in the breakdown of substances extracted from food. Here we applied a candidate gene approach to investigate whether in populations with different modes of subsistence, diet-related genetic adaptations could be identified in the genes AGXT, PLRP2, MTRR, NAT2 and CYP3A5.

Results

At CYP3A5, strong signatures of positive selection were detected, though not connected to any dietary variable, but instead to an environmental factor associated with the Tropic of Cancer. Suggestive signals of adaptions that could indeed be connected with differences in dietary habits of populations were only found for PLRP2 and NAT2. Contrarily, the demographic history of human populations seemed enough to explain patterns of diversity at AGXT and MTRR, once both conformed the evolutionary expectations under selective neutrality.

Conclusions

Accumulated evidence indicates that CYP3A5 has been under adaptive evolution during the history of human populations. PLRP2 and NAT2 also appear to have been modelled by some selective constrains, although clear support for that did not resist to a genome wide perspective. It is still necessary to clarify which were the biological mechanisms and the environmental factors involved as well as their interactions, to understand the nature and strength of the selective pressures that contributed to shape current patterns of genetic diversity at those loci.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0212-1) contains supplementary material, which is available to authorized users.

Implementation of new recommendations for the diagnosis of gestational diabetes: a 5-month audit

BACKGROUND

Recent international recommendations for the diagnosis of gestational diabetes (GD) were implemented in a university hospital. The aim was to audit the appropriateness of use of the new diagnostic approach.

METHODS

The same 5-month period, one before [2009, traditional two-step oral glucose tolerance test (OGTT) approach, S1] and one after the implementation of new criteria (2010, S2) were compared.

RESULTS

In the two periods, 256 (S1) and 245 (S2) pregnant women were examined and 298 (50 g, n = 195; 100 g, n = 103) and 252 (75 g) OGTTs were, respectively, executed. In S1, 54 (27.7% ) 50 g OGTTs resulted positive and 36 (66.7% ) of those performed the 100 g OGTT. In addition, three (1.5% of total) 50 g OGTT negative women were submitted to 100 g OGTT. Sixty-three women did 100 g OGTT only. In total, 14 (13.6% ) 100 g OGTTs were positive. In S2, 38 (15.1% ) 75 g OGTTs were positive. In women who did the complete protocol in the hospital, 98.3% in S1 and 77.0% in S2 performed the correct protocol (p < 0.0001).

CONCLUSIONS

In this hospital new recommendations for GD diagnosis are not correctly applied in 23% of cases. The main issue seems to be the lack of consideration of the new threshold for fasting glycemia (5.1 mmol/L) as a main decisional driver for performing OGTT.

[Global expression of Chagas´ disease - emerging opportunities and impact in Portugal]

Chagas disease, caused by the protozoan Trypanosoma cruzi is endemic in the countries of Central and South America. Despite vector control programs and other measures taken in the blood banks and maternity hospitals, it is estimated that there are about eight million people infected worldwide. Although traditionally associated with rural life and poverty, the current migration flows transform it into a global public health problem. In Portugal, this problem is poorly known, with an estimated underdiagnosis index that exceeds 99%. In European countries, besides imported cases, autochthonous infections arise through vertical transmission and blood/organ donation.The conventional serological tests for diagnosing Chagas disease and verifying its cure are indirect hemagglutination (IHA), indirect immunofluorescence (IFAT), and enzyme-linked immunoabsorbent assay (ELISA).The hypothesis of autoimmunity as a basic mechanism of this disease and the absence of early markers of cure are the causes of controversy regarding the specific treatment of this disease. The currently available drugs have adverse effects on a large number of patients and parasitological efficacy in chronic disease is suboptimal.The authors reinforce the need of a high level of suspicion in patients with suggestive epidemiology and the need of populational screening of specific high risk groups.

Emerging and under-recognized Chagas cardiomyopathy in non-endemic countries

Due to recent population emigration movements, an epidemic of Chagas disease is currently menacing most developed countries. The authors report the case of a 53-year-old Brazilian woman living in Europe for the last 10 years who developed heart failure symptoms, having a previous symptomatic sinus node disease with a pacemaker implant at age of 40 years. The diagnosis was based on serology and myocardial biopsy and the patient was treated with nifurtimox. The authors emphasize the need of a high level of suspicion in patients with suggestive epidemiology and the need of populational screening of specific high risk groups. New treatment options are also discussed.

Refining the genetic portrait of Portuguese Roma through X-chromosomal markers

Due to differences in transmission between X-chromosomal and autosomal DNA, the comparison of data derived from both markers allows deeper insight into the forces that shape the patterns of genetic diversity in populations. In this study, we applied this comparative approach to a sample of Portuguese Roma (Gypsies) by analyzing 43 X-chromosomal markers and 53 autosomal markers. Portuguese individuals of non-Gypsy ancestry were also studied. Compared with the host population, reduced levels of diversity on the X chromosome and autosomes were detected in Gypsies; this result was in line with known patterns of genetic diversity typical of Roma groups. As a consequence of the complex demographic past of the Roma, during which admixture and genetic drift played major roles, the amount of linkage disequilibrium (LD) on the X chromosome in Gypsies was considerably higher than that observed in non-Gypsies. When the pattern of differentiation on the X chromosome was compared with that of autosomes, there was evidence for asymmetries in female and male effective population sizes during the admixture between Roma and non-Roma. This result supplements previous data provided by mtDNA and the Y chromosome, underlining the importance of using combined information from the X chromosome and autosomes to dissect patterns of genetic diversity. Following the out-of-India dispersion, the Roma acquired a complex genetic pattern that was influenced by drift and introgression with surrounding populations, with important contributions from both males and females. We provide evidence that a sex-biased admixture with Europeans is probably associated with the founding of the Portuguese Gypsies.

[Hepatitis C in drug addicts: access and treatment compliance]

Currently, hepatitis C is a serious public health problem. It is estimated that there are 180 million people with chronic infection by hepatitis C virus (HCV) worldwide and that the prevalence of this infection in the Portuguese population ranges between 1 and 1.5%. In Portugal, there are neither up-to-date guidelines for treatment, nor recommendations for the diagnosis and management of patients with HCV and, in particular, for the endovenous drug users. The present article gathers consensus information regarding clinical practice and suggests some guidelines to the management and treatment accessibility of drug addicted patients with chronic infection by HCV, in Portugal.

Reconstructing the Indian origin and dispersal of the European Roma: a maternal genetic perspective

Previous genetic, anthropological and linguistic studies have shown that Roma (Gypsies) constitute a founder population dispersed throughout Europe whose origins might be traced to the Indian subcontinent. Linguistic and anthropological evidence point to Indo-Aryan ethnic groups from North-western India as the ancestral parental population of Roma. Recently, a strong genetic hint supporting this theory came from a study of a private mutation causing primary congenital glaucoma. In the present study, complete mitochondrial control sequences of Iberian Roma and previously published maternal lineages of other European Roma were analyzed in order to establish the genetic affinities among Roma groups, determine the degree of admixture with neighbouring populations, infer the migration routes followed since the first arrival to Europe, and survey the origin of Roma within the Indian subcontinent. Our results show that the maternal lineage composition in the Roma groups follows a pattern of different migration routes, with several founder effects, and low effective population sizes along their dispersal. Our data allowed the confirmation of a North/West migration route shared by Polish, Lithuanian and Iberian Roma. Additionally, eleven Roma founder lineages were identified and degrees of admixture with host populations were estimated. Finally, the comparison with an extensive database of Indian sequences allowed us to identify the Punjab state, in North-western India, as the putative ancestral homeland of the European Roma, in agreement with previous linguistic and anthropological studies.

A genetic historical sketch of European Gypsies: The perspective from autosomal markers

In this study, 123 unrelated Portuguese Gypsies were analyzed for 15 highly polymorphic autosomal short tandem repeats (STRs). Average gene diversity across the 15 markers was 76.7%, which is lower than that observed in the non-Gypsy Portuguese population. Subsets of STRs were used to perform comparisons with other Gypsy and corresponding host populations. Interestingly, diversity reduction in Gypsy groups compared to their non-Gypsy surrounding populations apparently varied according to an East-West gradient, which parallels their dispersion in Europe as well as a decrease in complexity of their internal structure. Analysis of genetic distances revealed that the average level of genetic differentiation between Gypsy groups was much larger than that observed between the corresponding non-Gypsy populations. The high rate of heterogeneity among Gypsies can be explained by strong genetic drift and limited intergroup gene flow. However, when genetic relationships were addressed through principal component analysis, all Gypsy populations clustered together and was clearly distinguished from other populations, a pattern that suggests their common origin. Concerning the putative ancestral genetic component, admixture analysis did not reveal strong Indian ancestry in the current Gypsy gene pools, in contrast to the high admixture estimates for either Europeans or Western Asians.

Differences in hepatitis C virus (HCV)-specific CD8 T-cell phenotype during pegylated alpha interferon and ribavirin treatment are related to response to antiviral therapy in patients chronically infected with HCV

CD8 T cells play a major role in antiviral immune responses. Their importance for progression to chronic hepatitis C and response to treatment are still unclear. To address these issues, hepatitis C virus (HCV)-specific CD8 T-cell responses were monitored, at the single-cell level, using HLA class I pentamers specific for HCV core and HCV NS3 epitopes, in 23 chronically infected patients during treatment with pegylated alpha interferon and ribavirin. Patients who presented a sustained-response to therapy had stronger HCV-specific CD8 T-cell responses at all time points studied. Moreover, there were clear differences in the phenotypes of these cells during therapy: in responder patients, terminally differentiated effector cells increased more rapidly, and their frequency was always higher than in nonresponder patients. Sustained-responder patients also showed a higher frequency of HCV-specific CD8 T cells producing cytotoxic factors. Overall, a late and inefficient differentiation process of HCV-specific CD8 T cells might be associated with lack of response to treatment. A better knowledge of the mechanisms underlying this impairment may be important for the development of new therapeutic strategies to maintain, restore, or increase CD8 T-cell effectiveness in chronic HCV infection.