Genetic and methylation status of CDKN2A (p14ARF/p16INK4A) and TP53 genes in recurrent respiratory papillomatosis.

Recurrent respiratory papillomatosis (RRP) is a rare and chronic disease affecting the upper airway with papillomatous lesions caused by the human papillomavirus (HPV) infection, especially HPV-6 and/or HPV-11 types. Little is known about the genetic and epigenetic drivers in RRP pathophysiology. For this purpose, we analyzed 27 papillomatous lesions from patients with RRP to evaluate somatic mutations and methylation status in CDKN2A (p14ARF/p16INK4A) and TP53, which are key tumor suppressor genes for the cell cycle control. Sanger sequencing analysis revealed one somatic mutation in TP53 (c.733_734insA) and four mutations in CDKN2A (c.-30G > T, c.29_30insA, c.69delT, and c.300C > A). These mutations were observed in 10 patients, 6 of which carried double mutation. Furthermore, 50% (5/10) of these patients carrying somatic mutations had RRP severity, representing 62.5% (5/8) of the severity cases in this study, albeit no significant association was found between somatic mutations and disease severity. Methylation-specific polymerase chain reaction assays revealed p14ARF promoter hypermethylation in 100% of cases, followed by TP53 (96.3%) and p16INK4A (55.6%), suggesting the influence of HPV in the DNA methylation machinery. In conclusion, somatic mutations were not common events identified in patients with RRP. However, epigenetic modulation by high methylation rates, particularly for the p14ARF/TP53 pathway, seems to be in the course of RRP development.

Identification of a novel large deletion and other copy number variations in the CFTR gene in patients with Cystic Fibrosis from a multiethnic population.

BACKGROUND: Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR). There are over 2000 different pathogenic and non-pathogenic variants described in association with a broad clinical heterogeneity. The most common types of mutations in this gene are single nucleotide substitutions or small deletions and insertions. However, large rearrangements, such as large duplications or deletions, are also a possible cause of CF; these variations are rarely tested in routine screenings, and much of them remain unidentified in some populations, especially those with high ethnic heterogeneity. METHODS: The present study utilized the Multiplex Ligation-dependent Probe Amplification (MLPA) technique for the detection of duplications and deletions in 165 CF patients from the Rio de Janeiro State (Brazil), which after extensive mutational screening, still exhibited one or two unidentified CF alleles. RESULTS: Five patients with alterations in MLPA signals were detected. After validation, we identified three copy number variations, one large duplication (CFTRdup2-3) and two large deletions (CFTRdel25-26 and CFTRdel25-27-CTTNBP2). Two detected deletions were not validated. They were false positives caused by a small deletion of 18 base pairs (232del18) and a point mutation (S168L) in the probe binding site. CONCLUSION: Our results highlight the importance of screening for large rearrangements in CF cases with no or only one CFTR mutation defined.

Prevalence and clinical implications of low-risk human papillomavirus among patients with recurrent respiratory papillomatosis in Rio de Janeiro, Brazil.

OBJECTIVE: The aim of this study was to investigate the presence of human papillomavirus (HPV) in biopsy specimens from juvenile and adult patients with histopathological diagnosis of recurrent respiratory papillomatosis (RRP) treated in two public hospitals in Rio de Janeiro, Brazil. METHODS: We performed the detection and genotyping of HPV by PCR technique for the types 6, 11, 16, and 18 in biopsy specimens from 41 RRP patients. RESULTS: The juvenile onset RRP (JoRRP) corresponded to 61% and the adult onset RRP (AoRRP) corresponded to 39% of the study group. Prevalence of males was observed in both the adult (81.3%) and the juvenile (56%) groups. Lesions in the larynx were more frequent in the glottis (46%). Genotyping analysis only revealed patients with HPV-6 (34.1%), HPV-11(17.1%), and co-infection HPV-6 and -11 (48.8%). RRP severity was significantly associated with the JoRRP (p<0.001), with extralaryngeal disease and more surgeries. However, no significant association between RRP severity and HPV types was found. One co-infected patient in the JoRRP died due to the evolution of the disease with lung involvement. CONCLUSION: These results show the strong association of HPV-6 and/or HPV-11 types with RRP and could complement the diagnosis, prognosis, and therapies for these patients. In addition, the HPV vaccination should be encouraged to prevent the disease.

ACTN3 gene variants as potential phenotype and performance biomarkers in Brazilian sport horses training for eventing in a tropical climate.

The aim of this study was to look for mutations in the equine ACTN3 gene and to identify sequence variants that might be associated with the phenotype and performance of Brazilian sport horses training for events in a tropical climate. Among 17 such horses direct DNA sequencing and mutation analysis of the exon 15 and the intron-exon boundaries of ACTN3 revealed 2 new sequence variants in the ACTN3 intron 14-15, designated c.1681-86G > A and c.1681-129delA. Wild-type/deletion heterozygotes (A/del) had a lower mean subcutaneous fat layer in the region of the gluteus medius, as measured by ultrasonography, than the del/del homozygotes; the correlation was significant (P = 0.017). This single base-pair deletion in ACTN3 intron 14-15 may have resulted in metabolic changes that led to increased deposition of body fat in the homozygous state. However, neither sequence variant was correlated with the time to fatigue in a test on a high-speed treadmill with an incremental-speed protocol.

Le but de la présente étude était de vérifier pour la présence de mutations dans le gène ACTN3 équin et d'identifier des variants de séquence qui pourraient être associés avec le phénotype et la performance de chevaux de sport brésiliens qui s'entraînent pour des concours dans un climat tropical. Parmi 17 chevaux qui correspondent à ces critères, le séquençage direct de l'ADN et l'analyse de mutation de l'exon 15 et des frontières de l'intron-exon d'ACTN3 a révélé deux nouveaux variants de séquence dans l'intron 14­15 d'ACTN3, désigné c.1681­86G > A et c.1681­129delA. Chez les hétérozygotes type-sauvage/délétion (A/del) la moyenne de l'épaisseur de la couche de gras sous-cutané dans la région du gluteus medius était plus petite, telle que mesurée par échographie, que celle des homozygotes del/del; la corrélation était significative (P = 0,017). Cette délétion unique de paire de bases dans l'intron 14­15 d'ACTN3 pourrait avoir résulté dans des changements métaboliques qui auraient mené à une augmentation du dépôt de gras chez les homozygotes. Toutefois, aucun des variants de séquence n'était corrélé avec le temps de fatigue dans un test sur un tapis-roulant à haute vitesse avec un protocole d'augmentation de vitesse.(Traduit par Docteur Serge Messier).

Molecular epidemiology of HIV-1 in Venezuela: high prevalence of HIV-1 subtype B and identification of a B/F recombinant infection.

The authors assessed HIV-1 variability in two distinct areas of Venezuela (the capital Caracas and Margarita Island) through the analysis of blood specimens and clinical and epidemiologic data of 72 persons. Proviral DNA was evaluated through heteroduplex mobility assay (HMA) based on the envelope region. Additionally, FOK I restriction enzyme digestion assay was performed in all subtype B ED31/33 amplified products to check the presence of the typical Brazilian subtype B GWGR variant. Sequencing and phylogenetic analysis for C2-V3 region of gp120 was performed in selected cases. The vast majority of samples were found to belong to subtype B, with a North American/European RFLP profile. An F subtype HIV-1 based on the region was identified for the first time in Venezuela. Genetic analyses of the protease and reverse transcriptase fragments of this sample depicted a recombinant B/F genetic profile. The discrimination capacity of HIV-1 subtypes using the primer set ED3/14-ED31/33 among the Caracas samples was found to be higher than for those from Margarita Island. The authors' results point to relevant differences between the samples of continental and Caribbean regions of Venezuela, requiring further evaluation of larger samples.

High frequency of recombinant genomes in HIV type 1 samples from Brazilian southeastern and southern regions.

We describe the genetic variability of HIV-1 subtypes and recombinant genomes in samples from southeastern and southern Brazilian regions. Phylogenetic analysis of a subset of 34 samples (8F, 7B, 7C, 2D, 1A, and 9 B" variant) based on the DNA sequencing of the env gp120 and gp41, gag p17, and nef regions confirmed the presence of nine (26.5%) potentially HIV-1 recombinant genomes. From the eight C2-V3 gp120 subtype F samples, only two seem to be pure F. One of the samples, classified as B" in the C2-V3 gp120 and as B in gp41 had the gag and nef regions clustering with subtype C. Two of seven C2-V3 subtype C samples presented distinct recombinant patterns as Bgag/Cenv/Bnef and Bgag/Cenv/Cnef. Putative recombinant breakpoints were obtained for three samples presenting discordant subtypes (F/B) between gp120 and gp41 env fragments showing that similar breakpoints could be observed between two unlinked samples (95BRRJ014 and 96BRRJ101). A higher degree of polymorphism was verified in the analysis of a subtype A sample (98BRRS058) in the C2-V3/gp41 env fragment. The intrasubtype C distance was found to be lower than that found for the other subtypes for all genomic regions. These data confirm that distinct HIV-1 subtypes and recombinant forms are actively participating in the Brazilian AIDS epidemic, and that the subtype C was introduced more recently into southern Brazil.