Socioeconomic disparities and the genomic landscape of gastric cancer.

The genomic characteristics of Peruvian patients with gastric adenocarcinoma from diverse socioeconomic backgrounds were examined in consideration of the possibility that patients from different socioeconomic backgrounds may be exposed to different risk factors. We conducted a prospective pilot study in two Peruvian cities (Lima and Ica). This study enrolled 15 patients from low socioeconomic status (LSES) and 15 patients from medium/high socioeconomic status (MHSES). The genomic profiling of gastric adenocarcinoma samples was done through the FoundationOne CDx platform. We compared the genomic characteristics and the need for targeted therapy and immunotherapy between LSES and MHSES. The genes with higher rates of alterations were TP53 (73.3% vs. 50.0%, P = 0.2635); CDH1 (26.7% vs. 28.6%, P = 1); CDKN2A (20.0% vs. 28.6%, P = 1); KRAS (33.3% vs. 7.1%, P = 0.1686); ARID1A (20.0% vs. 14.3%, P = 1); MLL2 (13.3% vs. 21.4%, P = 1) and SOX9 (33.3% vs. 0.0%, P = 0.0421) in LSES versus HMSES, respectively. There was no significant difference in tumor mutational burden (P = 0.377) or microsatellite status (P = 1). The LSES group had a higher need for targeted therapy or immunotherapy according to gene involvement and alterations. A significant genomic difference exists among patients with gastric adenocarcinoma of different socioeconomic status, which may result in a different need for targeted therapy and immunotherapy.

Characteristics of gastric cancer around the world.

Gastric cancer is one of the most important malignancies in the world due to the high burden of disease and lethality. In this work, we compared the main characteristics of gastric cancer between different regions of the world. We reviewed public repositories to retrieve epidemiological, molecular, clinicopathological, and risk factor data. Eastern Asia presents the highest incidence of gastric cancer, followed by eastern and central Europe. Intestinal histology was more frequent in Caucasians, while gastric tumors located in the cardias were less frequent in Africa and Latin America. TP53, LRP1B, and ARID1A are consistently the most frequently altered genes in all population groups. Gastric cancer is most frequent in men. African patients tend to be younger and have a higher proportion of women patients. Different patterns can be observed in the presentation of gastric cancer between different regions of the world. More research is needed in Latin America and Africa since these populations are underrepresented.

Design of a predicted MHC restricted short peptide immunodiagnostic and vaccine candidate for Fowl adenovirus C in chicken infection.

Fowl adenoviruses (FAdVs) are the ethiologic agents of multiple pathologies in chicken. There are five different species of FAdVs grouped as FAdV-A, FAdV-B, FAdV-C, FAdV-D, and FAdV-E. It is of interest to develop immunodiagnostics and vaccine candidate for Peruvian FAdV-C in chicken infection using MHC restricted short peptide candidates. We sequenced the complete genome of one FAdV strain isolated from a chicken of a local farm. A total of 44 protein coding genes were identified in each genome. We sequenced twelve Cobb chicken MHC alleles from animals of different farms in the central coast of Peru, and subsequently determined three optimal human MHC-I and four optimal human MHC-II substitute alleles for MHC-peptide prediction. The potential MHC restricted short peptide epitope-like candidates were predicted using human specific (with determined suitable chicken substitutes) NetMHC MHC-peptide prediction model with web server features from all the FAdV genomes available. FAdV specific peptides with calculated binding values to known substituted chicken MHC-I and MHC-II were further filtered for diagnostics and potential vaccine epitopes. Promiscuity to the 3/4 optimal human MHC-I/II alleles and conservation among the available FAdV genomes was considered in this analysis. The localization on the surface of the protein was considered for class II predicted peptides. Thus, a set of class I and class II specific peptides from FAdV were reported in this study. Hence, a multiepitopic protein was built with these peptides, and subsequently tested to confirm the production of specific antibodies in chicken.

Naturally Occurring ß-Nicotinamide Adenine Dinucleotide-Independent Avibacterium paragallinarum Isolate in Peru.

The ß-nicotinamide adenine dinucleotide (NAD) requirement has been considered to be essential for the isolation of the causal agent of infectious coryza, Avibacterium paragallinarum. Nevertheless, NAD-independent reports from South Africa and Mexico dismissed this paradigm. It is now accepted that both NAD-dependent and NAD-independent agents are able to cause infectious coryza and thus belong to the species A. paragallinarum. Here, we report for the first time in Peru a NAD-independent isolate from broiler chickens with typical signs of infectious coryza that have received a trivalent inactivated vaccine against infectious coryza. The isolate was identified based on its morphology, biochemical and serologic tests, and PCR results. Partial 16S rRNA gene sequence analysis confirmed the isolate as A. paragallinarum. There have been no cases of NAD-independent A. paragallinarum isolates reported in South America. Increasing reports around the world highlight not only the need to reconsider the in vitro nutritional requirements of this species for its correct isolation but also the cross-protection conferred by commercial infectious coryza vaccines against NAD-independent isolates.

An evaluation of serotyping of Avibacterium paragallinarum by use of a multiplex polymerase chain reaction.

In the present study, the ability of a recently proposed multiplex polymerase chain reaction (mPCR) to determine the serogroups (A, B, and C) of Avibacterium paragallinarum was evaluated. A total of 12 reference strains and 69 field isolates of Av. paragallinarum from Ecuador, Mexico, Panama, and Peru were included in the study. With some exceptions (which were serotyped in the current study), all of the isolates and strains had been previously examined by 2 serotyping schemes (Page and Kume) or were the formal reference strains for the schemes. Three of 6 (50%) reference strains of serogroup A, 2 (100%) of serogroup B, and 1 of 4 (25%) reference strains of serogroup C were correctly serotyped by the mPCR. With the field isolates, the mPCR correctly recognized 16 of the 17 serogroup A isolates, 10 of the 12 serogroup B isolates, and 18 of the 37 serogroup C isolates. Overall, the specificity and sensitivity of the PCR test was as follows: 82.6% and 87.3% (serogroup A), 85.7% and 71.9% (serogroup B), and 46.3% and 100% (serogroup C). The poor performance of the mPCR in terms of recognition of serogroup C isolates (low sensitivity of 46.3%) and the relatively high level of uncertainty about the accuracy of the serogroup A and B results (specificity of 87.3% and 71.9%, respectively) means that the assay cannot be recommended as a replacement for conventional serotyping.

Genome sequence and comparative analysis of Avibacterium paragallinarum.

BACKGROUND: Avibacterium paragallinarum, the causative agent of infectious coryza, is a highly contagious respiratory acute disease of poultry, which affects commercial chickens, laying hens and broilers worldwide. METHODOLOGY: In this study, we performed the whole genome sequencing, assembly and annotation of a Peruvian isolate of A. paragallinarum. Genome was sequenced in a 454 GS FLX Titanium system. De novo assembly was performed and annotation was completed with GS De Novo Assembler 2.6 using the H. influenzae str. F3031 gene model. Manual curation of the genome was performed with Artemis. Putative function of genes was predicted with Blast2GO. Virulence factors were identified by comparison with the Virulence Factor Database. RESULTS: The genome obtained has a length of 2.47 Mb with 40.66% of GC content. Seventy five large contigs (>500 nt) were obtained, which comprised 1,204 predicted genes. All the contigs are available in Genbank [GenBank: PRJNA64665]. A total of 103 virulence factors, reported in the Virulence Factor Database, were found in A. paragallinarum. Forty four of them are present in 7 species of Haemophilus, which are related with pathogenesis, virulence and host immune system evasion. A tetracycline-resistance associated transposon (Tn10), was found in A. paragallinarum, possibly acting as a defense mechanism. DISCUSSION AND CONCLUSION: The availability of A. paragallinarum genome represents an important source of information for the development of diagnostic tests, genotyping, and novel antigens for potential vaccines against infectious coryza. Identification of virulence factors contributes to better understanding the pathogenesis, and planning efforts for prevention and control of the disease.

Prevalencia y factores asociados al asma en niños de 5 a 14 años de un área rural del sur del Perú / Prevalence and factors associated with asthma in children 5 to 14 years in a rural area in from southern Peru

Objetivos. Determinar la prevalencia y los factores asociados al asma en niños de 5 a 14 años de una zona rural en la provincia de Ica, Perú. Materiales y métodos. Se realizó un estudio transversal en niños de 5 a 14 años deldistrito de Santiago, Ica, en el año 2004. Se visitaron a las madres de los niños seleccionados a través de un muestreo aleatorio sistemático y se aplicó un cuestionario basado en el ISAAC, asimismo, se evaluaron factores asociados al asma. Tomando el desarrollo de asma como variable de respuesta, se efectuó un modelo de regresión logística binaria a fin de identificar los factores que se le asocian de manera independiente. Resultados. De un total de 200 sujetos, 186fueron encuestados, 25 de ellos cumplían la definición de asma, la prevalencia global de asma fue de 13,5 por ciento (IC95 por ciento: 8,8 - 19,8 por ciento), predominando ligeramente en los niños menores de 5 años (39 por ciento) respecto al resto de grupos de edad (16 y 7 por ciento para 6 a 10 y 11 a 14 años respectivamente). Dentro de los factores asociados a tener asma se encontraron el antecedente de padecer rinitis, haber recibido antibióticos durante el primer año de vida y tabaquismo del padre enel primer año de vida. Los factores protectores fueron haber tenido diarrea durante el primer año de vida y haber sido vacunados con BCG. Conclusiones. La prevalencia de asma en una zona rural es comparable con la de otras ciudades en el mundo. Se le asocian factores que pueden ser modificados como el tratamiento antibiótico durante el primer año de vida y el tabaquismo paterno.

Objectives. To determine the prevalence and associated factors related to asthma in children aged from 5 to 14 years old in a rural province of Ica, Peru. Material and methods. A cross-sectional survey was carried out in children aged from 5 to 14 years old in Santiago, Ica, Peru during the year 2004. Childrens mothers were selected through systematic random sampling and interviewed using a pre-defined questionnaire based in ISAAC; we also recorded other datarelated to previous risk factors of asthma. As dependent variable, asthma development was used to perform a logistic regression model to identify associated factors. Results. We interviewed 186 of 200 sampled subjects, 25 of them met asthma criteria, so the global prevalence was 13.5 per cent (95 per cent CI: 8.8 û 19.8 per cent), predominating in children aged 5 years (39 per cent) comparing to other age strata (16 y 7 per cent for 6 to 10 years and 11 to 14 respectively). Identified factors associated to asthma included: previous diagnosed rhinitis, ever having received antibiotics and fathers smoking habit during the first year of life. Protective factors were: to have had diarrhea during the first year of life and having received BCG vaccine. Conclusions. The prevalence of asthma in this rural area is similar to that of other cities in the world. Furthermore, there are factors that can be changed, like to receive antibiotic during the first year of life and father smoking.