Nasal T-cell lymphoma presenting as midline lethal granuloma. Characterization of three cases by clinical markers of lymphomas

The authors report on three cases of so-called midline granuloma submitted to clinicopathologic and immunophenotype studies. The histopathologic features detected were necrosis, vasculitis and an atypical lymphohistiocytic infiltrate. Immunophenotype studies using monoclonal antibodies showed evidence leading to the diagnosis of nasal T cell lymphoma or lymphomatoid granulomatosis. Two of the patients with the presence of progressive or large cells died within 24 months, indicating that the size of the atypical lymphoid cells may be of prognostic significance.

Charcot foot: Skin temperature as a good clinical parameter for predicting disease outcome

Twenty-eight diabetics presenting with acute Charcot foot were immobilized and the temperature difference between limbs measured at each month. All patients had monthly follow-up visits for a year and the relapse rate was zero. We found that skin temperature is a good parameter to ensure safe immobilization withdrawal. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

Transcriptional Alterations Related to Neuropathology and Clinical Manifestation of Alzheimer's Disease

Alzheimer's disease (AD) is the most common cause of dementia in the human population, characterized by a spectrum of neuropathological abnormalities that results in memory impairment and loss of other cognitive processes as well as the presence of non-cognitive symptoms. Transcriptomic analyses provide an important approach to elucidating the pathogenesis of complex diseases like AD, helping to figure out both pre-clinical markers to identify susceptible patients and the early pathogenic mechanisms to serve as therapeutic targets. This study provides the gene expression profile of postmortem brain tissue from subjects with clinic-pathological AD (Braak IV, V, or V and CERAD B or C; and CDR >= 1), preclinical AD (Braak IV, V, or VI and CERAD B or C; and CDR = 0), and healthy older individuals (Braak <= II and CERAD 0 or A; and CDR = 0) in order to establish genes related to both AD neuropathology and clinical emergence of dementia. Based on differential gene expression, hierarchical clustering and network analysis, genes involved in energy metabolism, oxidative stress, DNA damage/repair, senescence, and transcriptional regulation were implicated with the neuropathology of AD; a transcriptional profile related to clinical manifestation of AD could not be detected with reliability using differential gene expression analysis, although genes involved in synaptic plasticity, and cell cycle seems to have a role revealed by gene classifier. In conclusion, the present data suggest gene expression profile changes secondary to the development of AD-related pathology and some genes that appear to be related to the clinical manifestation of dementia in subjects with significant AD pathology, making necessary further investigations to better understand these transcriptional findings on the pathogenesis and clinical emergence of AD.

Evaluation of epidemiological and clinical factors in survival of patients with de novo myelodysplastic syndrome at the University of Texas MD Anderson cancer center

Little is known about epidemiological markers that are associated with survival of patients with myelodysplastic syndromes (MDS). We conducted a secondary case-based analysis of 465 de novo MDS patients from the University of Texas MD Anderson Cancer Center (UTMDACC). We investigated the association between demographic as well as occupational exposure markers and survival while incorporating known clinical markers of prognosis. In our patient population, 60.6% were men and the majority were white (93.1%). The distribution of MDS subtypes by the French–American–British (FAB) classification was 81 (19%) refractory anemia (RA), 46 (9.9%) refractory anemia with ringed sideroblasts (RARS), 57 (12.3%) chronic myelomonocytic leukemia (CMML), 173 (37.2%) RA with excess blasts (RAEB), and 86 (18.5%) RAEB in transformation (RAEBT). We found that those older at diagnosis (> 60 years of age) (HR = 1.68, CI = 1.26-2.25) were at a higher risk of dying compared to younger patients. Similarly, high pack years of smoking (>= 30 pack years of smoking) (HR = 1.34, CI = 1.02-1.74), and agricultural chemical exposure (HR = 1.61, CI = 1.05-2.46) were significantly associated with overall lower survival when compared to patients with none or medium exposures. Among clinical markers, greater than 5% bone marrow blasts (HR = 1.81 CI = 1.27-2.56), poor cytogenetics (HR = 3.20, CI = 2.37-4.33)), and platelet cytopenias (<100000/ul) (HR = 1.46, CI = 1.11-1.92) were also significantly associated with overall MDS survival.^ The identification of epidemiological markers could help physicians stratify patients and customize treatment strategies to improve the outcome of MDS based on patient lifestyle information such as smoking exposure and agrochemical exposure. We hope that this study highlights the impact of these exposures in MDS prognosis.^

Ocular and systemic markers for vascular function in those at risk of type 2 diabetes mellitus and cardiovascular disease

The devastating impact of Type 2 Diabetes Mellitus (T2DM) -related morbidity and mortality on global healthcare is escalating with higher prevalences of obesity, poor diet, and sedentary lifestyles. Therefore, the clinical need for early diagnosis and prevention in groups of high-risk individuals is necessary. The purpose of this thesis was to investigate the use of surrogate markers, namely retinal vascular function, to determine future vascular endothelial dysfunction, atherosclerosis, large vessel disease and cardiovascular risk in certain groups. This namely covered normoglycaemic and normotensive South Asians (SAs), those with Impaired-Glucose Tolerance (IGT) and individuals with a familial history (FH) of T2DM. Additionally the effect of overweight and obesity was studied. The techniques and modified protocols adopted for this thesis involved the investigation of endothelial function by means of vascular reactivity at the ocular and systemic level. Furthermore, the relationships between retinal and systemic function with circulating markers for endothelial cell function and cardiovascular risk markers were explored. The principal studies and findings of the research were: Vascular Function in Normoglycaemic Individuals with and without a FH of T2DM WE FH individuals exhibited higher levels of total cholesterol levels that correlated well with the retinal arterial dilation amplitude to flicker light stimulus. However this did not extend to noticeable differences in markers for endothelial cell damage and impaired retinal and systemic function. Vascular Function in Normoglycaemic South-Asians vs. White-Europeans without a FH and Vascular Disturbances Compared to healthy WEs (normo -glycaemic and -tensive), SA participants exhibited levels of dyslipidaemia and a state of oxidative stress that extended to impaired vascular function as detected by reduced brachial artery flow-mediated dilation, slower retinal arterial vessel dilation reaction times (Appendix 3) and steeper constriction profiles. Furthermore, gender sub-group analysis presented in a sub-chapter shows that SA males demonstrated 24-hour systemic blood pressure (BP) and heart rate variability (HRV) abnormalities and heightened cardiovascular disease (CVD) risk. Vascular Function in Individuals Newly Diagnosed with IGT as compared to Normoglycaemic Healthy Controls Newly-diagnosed WE and SA IGT patients showed a greater risk for CVD and T2DM progression by means of 24-hour BP abnormalities, dyslipidaemia, increased carotid artery intimal-media thickness (c-IMT), Framingham scores and cholesterol ratios. Additionally, pre-clinical markers for oxidative stress and endothelial dysfunction, as evident by significantly lower levels of plasma glutathione and increased levels of von-Willebrand factor in IGT individuals, extended to impaired vascular systemic and retinal function compared to normal controls. This originally shows retinal, systemic and biochemical disturbances in newly-diagnosed IGT not previously reported before. Vascular Function in Normal, Overweight and Obese Individuals of SA and WE Ethnicity In addition to the intended study chapters, the thesis also investigated the influence of obesity and overweight on vascular function. Most importantly, it was found for the first time that compared to lean individuals it was overweight and not obese individuals that exhibited signs of vascular systemic and ocular dysfunction that was evident alongside markers of atherosclerosis, CVD risk and endothelial damage.

Detection of tissue plasminogen activator (t-PA) and plasminogen activator inhibitor 2(PAI-2) in gingival crevicular fluid from healthy, gingivitis and periodontitis patients

Background: The regulation of plasminogen activation is a key element in controlling proteolytic events in the extracellular matrix. Our previous studies had demonstrated that in inflamed gingival tissues, tissue-type plasminogen activator (t-PA) is significantly increased in the extracellular matrix of the connective tissue and that interleukin 1β (IL-1β) can up regulate the level of t-PA and plasminogen activator inhibitor-2 (PAI-2) synthesis by human gingival fibroblasts. Method: In the present study, the levels of t-PA and PAI-2 in gingival crevicular fluid (GCF) were measured from healthy, gingivitis and periodontitis sites and compared before and after periodontal treatment. Crevicular fluid from106 periodontal sites in 33 patients were collected. 24 sites from 11 periodontitis patients received periodontal treatment after the first sample collection and post-treatment samples were collected 14 days after treatment. All samples were analyzed by enzyme-linked immunosorbent assay (ELISA) for t-PA and PAI-2. Results: The results showed that significantly high levels of t-PA and PAI-2 in GCF were found in the gingivitis and periodontitis sites. Periodontal treatment led to significant decreases of PAI-2, but not t-PA, after 14 days. A significant positive linear correlation was found between t-PA and PAI-2 in GCF (r=0.80, p<0.01). In the healthy group, different sites from within the same subject showed little variation of t-PA and PAI-2 in GCF. However, the gingivitis and periodontitis sites showed large variation. These results suggest a good correlation between t-PA and PAI-2 with the severity of periodontal conditions. Conclusion: This study indicates that t-PA and PAI-2 may play a significant rôle in the periodontal tissue destruction and tissue remodeling and that t-PA and PAI-2 in GCF may be used as clinical markers to evaluate the periodontal diseases and assess treatment.

Real-life Social Attention in Children with Autism Spectrum Disorders

Autism is a neuro-developmental disorder defined by atypical social behaviour, of which atypical social attention behaviours are among the earliest clinical markers (Volkmar et al., 1997). Eye tracking studies using still images and movie clips have provided a method for the precise quantification of atypical social attention in ASD. This is generally characterised by diminished viewing of the most socially pertinent regions (eyes), and increased viewing of less socially informative regions (body, background, objects) (Klin et al., 2002; Riby & Hancock, 2008, 2009). Ecological validity within eye tracking studies has become an increasingly important issue. As of yet, however, little is known about the precise nature of the atypicalities of social attention in ASD in real-life. Objectives: To capture and quantify gaze patterns for children with an ASD within a real life setting, compared to two Typically Developing (TD) comparison groups. Methods: Nine children with an ASD were compared to two age matched TD groups – a verbal (N=9) and a non-verbal (N=9) comparison group. A real-life scenario was created involving an experimenter posing as a magician, and consisted of 3 segments: a conversation segment; a magic trick segment; and a puppet segment. The first segment explored children’s attentional preferences during a real-life conversation; the magic trick segment explored children’s use of the eyes as a communicative cue, and the puppet segment explored attention capture. Finally, part of the puppet section explored children’s use of facial information in response to an unexpected event. Results: The most striking difference between the groups was the diminished viewing of the eyes by the ASD group in comparison to both control groups. This was found particularly during the conversation segment, but also during the magic trick segment, and during the puppet segment. When in conversation, participants with ASD were found to spend a greater proportion time looking off-screen, in comparison to TD participants. There was also a tendency for the ASD group to spend a greater proportion of time looking to the mouth of the experimenter. During the magic trick segment, despite the fact that the eyes were not predictive of a correct location, both TD comparison groups continued to use the eyes as a communicative cue, whereas the ASD group did not. In the puppet segment, all three groups spent a similar amount of time looking between the puppet and regions of the experimenter’s face. However, in response to an unexpected event, the ASD group were significantly slower to fixate back on the experimenter’s face. Conclusions: The results demonstrate the reduced salience of socially pertinent information for children with ASD in real life, and they provide support for the findings from previous eye tracking studies involving scene viewing. However, the results also highlight a pattern looking off-screen for both the TD and ASD groups. This eye movement behaviour is likely to be associated specifically with real-life interaction, as it has functional relevance (Doherty-Sneddon et al., 2002). However, the fact that it is significantly increased in the ASD group has implications for their understanding of real life social interactions.

Durée de lʼexposition avec symptômes, séquelles et coûts de lʼasthme professionnel en relation avec le statut psychologique et socioéconomique

Le facteur le plus important de pronostic de l'asthme professionnel (AP) est la durée des symptômes avant le retrait de lʼexposition à lʼagent causant lʼAP. La qualité de vie réduite, la détresse psychologique et les maladies psychiatriques sont des conditions souvent associées à l'AP. Notre objectif était d'identifier les facteurs, incluant le statut socioéconomique, qui ont une influence sur lʼintervalle de temps nécessaire pour présenter une requête à une agence médicolégale à la suite de lʼapparition de symptômes dʼasthme et de confirmer qu'un tel délai est associé à un moins bon pronostic respiratoire et à des coûts directs plus élevés. En outre, nous avons examiné la relation entre les variables cliniques et socio-économiques dʼune part et leur influence sur les facteurs psychologiques et économiques dʼautre part chez des travailleurs atteints d'AP. Ensuite, nous avons voulu évaluer si les individus souffrant de détresse psychologique (DP) et de morbidité psychiatrique pourraient être identifiés en utilisant un instrument mesurant la qualité de vie (QV). Lʼétude a été effectuée auprès dʼindividus ayant déposé des demandes d'indemnisation pourʼAP auprès du Commission de la sécurité et de la santé du travail du Québec (CSST). Les données ont été recueillies au moment de la réévaluation, soit environ deux ans et demi après le diagnostic. Outre la collecte des marqueurs cliniques de l'asthme, les individus ont été soumis à une évaluation générale de leur histoire sociodémographique et médicale, à une brève entrevue psychiatrique (évaluation des soins primaires des troubles mentaux, PRIME-MD) et à un ensemble de questionnaires, incluant le Questionnaire sur la qualité de vie - AQLQ(S), le Questionnaire respiratoire de St. George (SGRQ) et le Psychiatric Symptom Index (PSI).Soixante personnes ont été incluses dans l'étude. Etre plus âgé, avoir un revenu supérieur à 30 000$ CA etêtre atteint dʼAP dû à un allergène de haut poids moléculaire ont une association positive avec le nombre dʼannées dʼexposition avec symptômes avant le retrait. Au cours de la période de suivi, le nombre dʼannées dʼexposition avec symptômes était plus grand chez les individus ayant une hyperréactivité bronchique persistante. Par ailleurs, la présence de symptômes au poste de travail pendant moins d'un an est associée à une réduction des coûts directs. Les paramètres de QV et de DP avaient des corrélations modérées avec les marqueurs cliniques de lʼAP. Les plus fortes associations avec ces variables ont pu être observées dans les cas de la sévérité de l'asthme, des statuts dʼemploi et matrimonial, du revenu et de la durée de la période de travail avec l'employeur. Un seuil de 5,1 au niveau de la sous-échelle de la fonction émotionnelle de lʼAQLQ(S) sʼest avéré avoir la meilleure valeur discriminante pour distinguer les individus avec ou sans détresse psychiatrique cliniquement significative selon le PSI. Nous avons été en mesure d'identifier les variables socio-économiques associées à un intervalle plus long dʼexposition professionnelle en présence de symptômes dʼasthme. De même, une plus longue période d'exposition a été associée à un moins bon pronostic de la maladie et à des coûts de compensation plus élevés. Ces résultats s'avèrent utiles pour la surveillance de lʼAP qui pourrait cibler ces sous-groupes d'individus. La QV et la PS sont fréquemment réduites chez les individus atteints d'AP qui perçoivent une compensation. Elles sont associées à des marqueurs cliniques de lʼasthme et à des facteurs socio-économiques. En outre, nos résultats suggèrent que le questionnaire de lʼAQLQ(S) peut être utilisé pour identifier les individus avec un niveau de détresse psychologique potentiellement significatif.

Epigenetics and autoimmune diseases

Epigenetics is defined as the study of all inheritable and potentially reversible changes in genome function that do not alter the nucleotide sequence within the DNA. Epigenetic mechanisms such as DNA methylation, histone modification, nucleosome positioning, and microRNAs (miRNAs) are essential to carry out key functions in the regulation of gene expression. Therefore, the epigenetic mechanisms are a window to understanding the possible mechanisms involved in the pathogenesis of complex diseases such as autoimmune diseases. It is noteworthy that autoimmune diseases do not have the same epidemiology, pathology, or symptoms but do have a common origin that can be explained by the sharing of immunogenetic mechanisms. Currently, epigenetic research is looking for disruption in one or more epigenetic mechanisms to provide new insights into autoimmune diseases. The identification of cell-specific targets of epigenetic deregulation will serve us as clinical markers for diagnosis, disease progression, and therapy approaches.

Estado nutricional e marcadores clínico-bioquímicos em indivíduos portadores de carcinoma gastrointestinal

O estado nutricional de indivíduos portadores de carcinoma gastrointestinal é frequentemente afetado, sendo agravado em função da carcinogênese promover ativação do processo inflamatório e consequente ativação do sistema imunológico, com produção de citocinas e proteínas de fase aguda, como proteína C- reativa, que resulta no hipermetabolismo, acelerando a perda de peso e progredindo para o quadro de caquexia. Este trabalho teve como objetivo analisar o estado nutricional e os marcadores clínico-bioquímicos em indivíduos portadores de carcinoma gastrointestinal, atendidos no Hospital Universitário João de Barros Barreto (HUJBB), em Belém-PA. Foi realizado estudo transversal, descritivo, observacional com pacientes adultos e idosos, portadores de carcinoma gastrointestinal atendidos na Unidade de Alta Complexidade em Oncologia e na clínica cirúrgica do HUJBB, no período de dezembro de 2013 a julho de 2014. Realizou-se avaliação nutricional por meio de parâmetros antropométricos, que incluíram índice de massa corporal (IMC), percentual de perda de peso (%PP), circunferência do braço (CB), circunferência muscular do braço (CMB), área muscular do braço corrigida (AMBc), prega cutânea triciptal (PCT) e músculo adutor do polegar (MAP), parâmetros bioquímicos, por meio da classificação da hemoglobina, contagem total de linfócitos (CTL), albumina, transferrina, índice de prognóstico inflamatório-nutricional (IPIN) e parâmetros subjetivos, utilizando-se a avaliação subjetiva global produzida pelo paciente (ASG-PPP), além da identificação e classificação da caquexia. Foram avaliados 44 pacientes, sendo 63,30% do sexo masculino com idade média de 61,2 anos (±13,3). 95,50% eram naturais do Pará, 45,50% residentes no interior, 50,00% apresentavam escolaridade em ensino fundamental incompleto e 52,30% não possuíam renda familiar. Do total de pacientes avaliados, 63,60% possuíam neoplasia de estômago; destes, 50,00% estavam em estádio clínico IV e 73,30% em tratamento cirúrgico, com tempo médio de internação de 45,85 dias (±32,97). Na avaliação nutricional, verificou-se 20,50% de eutrofia para adultos e 42,30% para idosos, por meio do IMC, porém, em avaliação isolada dos compartimentos muscular e adiposo, verificou-se 59,10% de depleção grave por meio da AMBc, 54,50% por meio da PCT e 75,00% com presença de depleção em algum grau em CB e 68,18% em CMB. A perda de peso grave foi verificada em 61,36% dos pacientes avaliados e no MAP, obteve-se maior prevalência de depleção moderada (30,20%). Nos parâmetros bioquímicos, observou-se redução grave em hemoglobina em 61,40% dos pacientes, depleção leve em CTL em 56,80%, de albumina em 47,70% e depleção moderada de transferrina em 45,50%. Na avaliação do IPIN, verificou-se médio risco de complicação para 56,80% dos pacientes avaliados. Na ASG-PPP, 63,60% dos pacientes foram classificados em desnutrição grave e a presença de caquexia sintomática foi de 54,50%. No que se refere à análise de correlação, constatou-se que houve correlação positiva e significativa de IMC com CMB, CB, PCT, AMBc, MAP e Hemoglobina; CMB com CB e AMBc; CB com PCT, AMBc, MAP, e hemoglobina; PCT com AMBc; AMBc com MAP. Na análise de componente principal, verificou-se como métodos mais sensíveis para a detecção de desnutrição a avaliação de CB, AMBc, CMB, IMC, PCT, MAP, IPIN e avaliação da caquexia. Desta forma, os resultados obtidos no presente estudo evidenciam o comprometimento nutricional em pacientes portadores de carcinoma gastrointestinal, por diferentes parâmetros, demonstrando assim que a desnutrição ocorre de forma global, com perdas tanto de tecido adiposo quanto de tecido muscular, assim como alterações a nível bioquímico.

Functional Limitation and Intermittent Claudication: Impact of Blood Pressure Measurements

Background: Arterial hypertension is an important risk factor for Lower-Limb Occlusive Arterial Disease (LLOAD). However, the correlation between blood pressure and pulse pressure (PP) with LLOAD severity and functional impairment resulting from this disease is not well established in the Brazilian population. Objective: To verify whether there is a correlation between blood pressure, PP, LLOAD severity and functional capacity in patients with symptomatic LLOAD. Methods: A total of 65 patients (62.2 + 8.1 years, 56.9% males) were evaluated. They were divided into two groups: normal (A) and high (B) blood pressure. LLOAD severity was assessed using the ankle-brachial index (ABI) and functional capacity by the total and pain-free walking distance at the 6-minute walking test (6MWT). Results: Group A consisted of 17 (26.1%) patients. The systolic (SBP), diastolic blood pressure (DBP), and PP were, respectively, 125.4 +/- 11.7, 74.5 +/- 9.1 and 50.9 +/- 10.0 mmHg in group A and 160.7 +/- 19.6, 90.0 +/- 12.2 and 70.7 +/- 20.2 mmHg in group B. The ABI was significantly lower in group B (0.66 +/- 0.12 vs. 0.57 +/- 0.13, p < 0.05). SBP and PP correlated with LLOAD severity and the distances walked at the 6MWT. Patients with PP > 40 mmHg walked shorter distances. Conclusion: SBP and PP significantly correlated with the distances walked in the 6MWT, suggesting they are clinical markers of functional capacity impairment in patients with symptomatic LLOAD. (Arq Bras Cardiol 2012; 98(2): 161-166)

Practicability of nitrogen multiple-breath washout measurements in a pediatric cystic fibrosis outpatient setting

BACKGROUND: Although lung clearance index (LCI) is a sensitive indicator of mild cystic fibrosis (CF) lung disease, it is rarely measured due to lengthy protocols and the commercial unavailability of multiple-breath washout (MBW) setups and tracer gases. We used a newly validated, commercially available nitrogen (N(2) ) MBW setup to assess success rate, duration, and variability of LCI within a 20 min timeframe, during clinical routine. We also evaluated the relationship between LCI and other clinical markers of CF lung disease. METHODS: One hundred thirty six children (83 with CF) between 4 and 16 years were studied in a pediatric CF outpatient setting. One hundred eighteen out of 136 children were naïve to MBW. Within 20 min, each child was trained, N(2) MBW was performed, and LCI was analyzed. We assessed intra- and between-test reproducibility in a subgroup of children. RESULTS: At least one LCI was feasible in 123 (90%) children, with a mean (range) of 3.3 (1.2-6.4) min per test. Two or more measurements were feasible in 56 (41%) children. Comparing LCI in CF versus controls, LCI mean (SD) was 12.0 (3.9) versus 6.1 (0.9), and the intra- and inter-test coefficient of repeatability was 1.00 versus 0.81 and 0.96 versus 0.62, respectively. LCI was correlated with spirometry, blood gases, and Pseudomonas aeruginosa infection. CONCLUSIONS: Using available N(2) MBW equipment, LCI measurements are practical and fast in children. LCI is correlated with markers of CF lung disease. Longer timeframes would be required for triplicate N(2) MBW tests in inexperienced children. Pediatr Pulmonol. © 2012 Wiley Periodicals, Inc.

Toward stratified treatments for bipolar disorders

In bipolar disorders, there are unclear diagnostic boundaries with unipolar depression and schizophrenia, inconsistency of treatment guidelines, relatively long trial-and-error phases of treatment optimization, and increasing use of complex combination therapies lacking empirical evidence. These suggest that the current definition of bipolar disorders based on clinical symptoms reflects a clinically and etiologically heterogeneous entity. Stratification of treatments for bipolar disorders based on biomarkers and improved clinical markers are greatly needed to increase the efficacy of currently available treatments and improve the chances of developing novel therapeutic approaches. This review provides a theoretical framework to identify biomarkers and summarizes the most promising markers for stratification regarding beneficial and adverse treatment effects. State and stage specifiers, neuropsychological tests, neuroimaging, and genetic and epigenetic biomarkers will be discussed with respect to their ability to predict the response to specific pharmacological and psychosocial psychotherapies for bipolar disorders. To date, the most reliable markers are derived from psychopathology and history-taking, while no biomarker has been found that reliably predicts individual treatment responses. This review underlines both the importance of clinical diagnostic skills and the need for biological research to identify markers that will allow the targeting of treatment specifically to sub-populations of bipolar patients who are more likely to benefit from a specific treatment and less likely to develop adverse reactions.

Adenocarcinoma da próstata incidental : um estudo retrospectivo

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains

Background The HIV virus is known for its ability to exploit numerous genetic and evolutionary mechanisms to ensure its proliferation, among them, high replication, mutation and recombination rates. Sliding MinPD, a recently introduced computational method [1], was used to investigate the patterns of evolution of serially-sampled HIV-1 sequence data from eight patients with a special focus on the emergence of X4 strains. Unlike other phylogenetic methods, Sliding MinPD combines distance-based inference with a nonparametric bootstrap procedure and automated recombination detection to reconstruct the evolutionary history of longitudinal sequence data. We present serial evolutionary networks as a longitudinal representation of the mutational pathways of a viral population in a within-host environment. The longitudinal representation of the evolutionary networks was complemented with charts of clinical markers to facilitate correlation analysis between pertinent clinical information and the evolutionary relationships. Results Analysis based on the predicted networks suggests the following:: significantly stronger recombination signals (p = 0.003) for the inferred ancestors of the X4 strains, recombination events between different lineages and recombination events between putative reservoir virus and those from a later population, an early star-like topology observed for four of the patients who died of AIDS. A significantly higher number of recombinants were predicted at sampling points that corresponded to peaks in the viral load levels (p = 0.0042). Conclusion Our results indicate that serial evolutionary networks of HIV sequences enable systematic statistical analysis of the implicit relations embedded in the topology of the structure and can greatly facilitate identification of patterns of evolution that can lead to specific hypotheses and new insights. The conclusions of applying our method to empirical HIV data support the conventional wisdom of the new generation HIV treatments, that in order to keep the virus in check, viral loads need to be suppressed to almost undetectable levels.