Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes

Background

Endogenous retroviruses (ERVs) are the result of the integration of retroviruses into host DNA following germline infection. Endogenous retroviruses are made up of three main genes: gag, pol, and env, each of which encodes viral proteins that can be conserved or not. ERVs have been observed in a wide range of vertebrate genomes and their functions are associated with viral silencing and gene regulation.

Results

In this work, we studied the evolutionary history of endogenous retroviruses associated with five human genes (INPP5B, DET1, PSMA1, USH2A, and MACROD2), which are located within intron sections. To verify the retroviral origin of the candidates, several approaches were used to detect and locate ERV elements. Both orthologous and paralogous genes were identified by Ensembl and then analyzed for ERV presence using RetroTector. A phylogenetic tree was reconstructed to identify the minimum time point of ERV acquisition. From that search, we detected ERVs throughout the primate lineage and in some other groups. Also, we identified the minimum origin of the ERVs from the parvorder Catarrhini to the Homininae subfamily.

Conclusions

With the data collected, and by observing the transcription factors annotated inside ERVs, we propose that these elements play a relevant role in gene expression regulation and they probably possess important features for tumorigenesis control.

[Uncommon presentation of psoriasis vulgaris in an 11-year-old patient]

Die Psoriasis vulgaris tritt mit einer Prävalenz von bis zu 2 % im Kindes- und Jugendalter auf. Größtenteils wird die Diagnose klinisch gestellt. Wir berichten über einen pädiatrischen Patienten, welcher uns aufgrund der für eine Psoriasis vulgaris eher untypischen Lokalisation vor eine diagnostische Herausforderung stellte. Diskutiert werden die wichtigsten Differenzialdiagnosen der verschiedenen Psoriasisformen sowie die aktuellen Therapieempfehlungen im Kindes- und Jugendalter.

Clinical variants of mycosis fungoides in a cohort

INTRODUCTION

Mycosis fungoides (MF) is the most common primary skin T-cell lymphoma, which is characterized for a heterogeneous clinical expressivity.

OBJECTIVE

To report clinical variants and sociodemographic characteristics in patients with MF under the care of a dermatological hospital.

METHODS

290 patients with MF clinical and histopathological diagnosis attended to over the course of 11 years were included. Sociodemographic description of patients was made, who were classified according to clinical and histopathological variants.

RESULTS

MF was recorded in 57.9 % of women and 42 % of men. The most common clinical variant was the classic type in 46.2 %; dyschromic variants accounted for 35.2 %, out of which hypopigmented MF was the most representative (17.6 %); poikilodermatous MF accounted for 4.1 %, and folliculotropic, for 3.1%. The papular variant occurred in six patients (2.1 %), the single-plaque variety in three (1%), and the ichthyosiform, syringotropic and granulomatous slack skin varieties occurred in one patient each. The granulomatous variant was found in 0.7 %, and 1.4 % had erythroderma.

CONCLUSIONS

The most common MF clinical variant was classic plaque stage, followed by dyschromic variants. Other clinical variants accounted for 18.6 %.

Molecular modeling in the age of clinical genomics, the enterprise of the next generation

Protein modeling and molecular dynamics hold a unique toolset to aide in the characterization of clinical variants that may result in disease. Not only do these techniques offer the ability to study under characterized proteins, but they do this with the speed that is needed for time-sensitive clinical cases. In this paper we retrospectively study a clinical variant in the XIAP protein, C203Y, while addressing additional variants seen in patients with similar gastrointestinal phenotypes as the C203Y mutation. In agreement with the clinical tests performed on the C203Y patient, protein modeling and molecular dynamics suggest that direct interactions with RIPK2 and Caspase3 are altered by the C203Y mutation and subsequent loss of Zn coordination in the second BIR domain of XIAP. Interestingly, the variant does not appear to alter interactions with SMAC, resulting in further damage to the caspase and NOD2 pathways. To expand the computational strategy designed when studying XIAP, we have applied the molecular modeling tools to a list of 140 variants seen in CFTR associated with cystic fibrosis, and a list of undiagnosed variants in 17 different genes. This paper shows the exciting applications of molecular modeling in the classification and characterization of genetic variants identified in next generation sequencing. Graphical abstract XIAP in Caspase 3 and NOD2 signaling pathways.