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1.
Cancer Med ; 2019 Dec 18.
Artigo em Inglês | MEDLINE | ID: mdl-31851786

RESUMO

BACKGROUND: Definitive chemoradiation therapy (dCRT) is the standard treatment for patients with nonsurgical esophageal squamous cell carcinoma (ESCC), yet patients have demonstrated great variations in their responses to dCRT and inevitably progressed following treatment. METHODS: To identify prognostic biomarkers, we performed targeted next-generation sequencing of 416 cancer-related genes on primary tumors from 47 nonsurgical ESCC patients prior to dCRT treatment. The association between genetic alterations and patients' local recurrence-free survival (LRFS), progression-free survival (PFS), and overall survival (OS) was analyzed. RESULTS: TP53 (78% of patients), NOTCH1 (32%), ARID1A (13%), FAT1 (13%), and CDKN2A (13%) were commonly mutated in ESCC patients, while gene amplifications frequently occurred in MCL1 (36%), FGF19 (34%), MYC (32%), CCND1 (27%), ZNF217 (15%), CDKN2A (13%), and YAP1 (11%). Univariate and multivariate analyses of clinical factors and genetic alterations indicated that sex is an independent prognostic factor, with males tending to have better LRFS (hazard ratio [HR], 0.25; 95%CI, 0.08-0.77, P = .015) and progression-free survival (PFS) (HR, 0.35; 95%CI, 0.13-0.93, P = .030) following dCRT. Meanwhile, YAP1 amplification (n = 7) was an adverse prognostic factor, and patients with this alteration demonstrated a tendency toward worse outcomes with shorter LRFS (HR, 4.06; 95%CI, 1.26-13.14, P = .019) and OS (HR, 2.78; 95%CI, 0.95-8.17, P = .062). In a subgroup analysis, while sex and M-stage were controlled, a much stronger negative effect of YAP1 amplification vs wild-type in LRFS was observed (log-rank P = .0067). CONCLUSION: The results suggested that YAP1 amplification is a potentially useful biomarker for predicting treatment outcomes and identifying patients with a high risk of relapse who should be closely monitored.

2.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(5): 3111-2, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-25707413

RESUMO

Yellowfin tuna (Thunnus albacares) is one of the most important economic fishes around the world. In the present study, we determined the complete mitochondrial DNA sequence and organization of T. albacares. The entire mitochondrial genome is a circular-molecule of 16,528 bp in length, which encodes 37 genes in all. These genes comprise 13 protein-coding genes (ATP6 and 8, COI-III, Cytb, ND1-6 and 4 L), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (12S and 16S rRNAs). The complete mitochondrial genome sequence of T. albacares can provide basic information for the studies on molecular taxonomy and conservation genetics of teleost fishes.


Assuntos
Genoma Mitocondrial , Genômica , Atum/classificação , Atum/genética , Animais , Composição de Bases , Códon , Genes Mitocondriais , Tamanho do Genoma , Genômica/métodos , Fases de Leitura Aberta , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
3.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(6): 4570-4571, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-26641714

RESUMO

In this study, we obtained the complete mitochondrial genome sequence of Sphyraena jello and analyzed its phylogenetic position. The complete mitogenome of S. jello is 16 699 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Among the 37 genes, 28 were encoded on heavy strand, while 9 were encoded on light strand. The overall base composition was 28.97% for A, 16.14% for G, 29.64% for C, and 25.25% for T, with a higher A + T content (54.22%). The phylogenetic analysis based on 13 concatenated protein-coding genes suggested that S. jello is a sister species to Sphyraena barracuda in the family Sphyraenidae. This result should be useful for understanding the genetic structure, molecular evolution, and phylogeny of S. jello and related species.


Assuntos
Genoma Mitocondrial , Perciformes/genética , Animais , Composição de Bases , Códon de Iniciação , DNA Mitocondrial/química , DNA Mitocondrial/isolamento & purificação , DNA Mitocondrial/metabolismo , Proteínas de Peixes/química , Proteínas de Peixes/genética , Proteínas de Peixes/metabolismo , Fases de Leitura Aberta/genética , Perciformes/classificação , Filogenia , RNA Ribossômico/química , RNA Ribossômico/genética , RNA de Transferência/química , RNA de Transferência/genética , Análise de Sequência de DNA
4.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(6): 4189-4190, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-25600736

RESUMO

Thunnus alalunga is an excellent food fish and is of great importance in recreational fisheries. In the study, the complete mitochondrial genome (mitogenome) of T. alalunga is sequenced and annotated, which is a circular DNA molecule with 16,527 bp in length. The overall nucleotide base composition of T. alalunga mitogenome is as follows: A, 28.37%; G, 16.69%; T, 25.46%; and C, 29.49%, with the A+T content of 53.83%, showing an obvious anti-G bias. The entire mitogenome encodes 37 genes in all, comprising 13 protein-coding genes (ATP6 and ATP8, COI-III, Cytb, ND1-6 and 4L), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (12S and 16S rRNAs). The complete mitochondrial genome sequence of T. alalunga can provide useful information for the studies on molecular systematics, stock evaluation, and conservation genetics of teleost fishes.


Assuntos
Proteínas de Peixes/genética , Peixes/genética , Genoma Mitocondrial , Proteínas Mitocondriais/genética , RNA Ribossômico/genética , RNA de Transferência/genética , RNA/genética , Animais , RNA Mitocondrial
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