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| 1 | Quasispecies structure,cornerstone of hepatitis B virus infection: Mass sequencing approach显示文摘Hepatitis B virus(HBV)is a DNA virus with complex replication,and high replication and mutation rates,leading to a heterogeneous viral population.The population is comprised of genomes that are closely related,but not identical;hence,HBV is considered a viral quasispecies.Quasispecies variability may be somewhat limited by the high degree of overlapping between the HBV coding regions,which is especially important in the P and S gene overlapping regions,but is less significant in the X and preCore/Core genes.Despite this restriction,several clinically and pathologically relevant variants have been characterized along the viral genome.Next-generation sequencing(NGS)approaches enable high-throughput analysis of thousands of clonally amplified regions and are powerful tools for characterizing genetic diversity in viral strains.In the present review,we update the information regarding HBV variability and present a summary of the various NGS approaches available for research in this virus.In addition,we provide an analysis of the clinical implications of HBV variants and their study by NGS. | Francisco Rodriguez-Frias Maria Buti David Tabernero Maria Homs | 2013 | World Journal of Gastroenterology2013，19，41： | 11 |
| 2 | Regorafenib monotherapy for previously treated metastatic colorectal cancer (CORRECT): an international, multicentre, randomised, placebo-controlled, phase 3 trial显示文摘 | Axel Grothey Eric Van Cutsem Alberto Sobrero Salvatore Siena Alfredo Falcone Marc Ychou Yves Humblet Olivier Bouché Laurent Mineur Carlo Barone Antoine Adenis Josep Tabernero Takayuki Yoshino Heinz-Josef Lenz Richard M Goldberg Daniel J Sargent Frank Ciho | 2012 | The Lancet2012，，： | 10 |
| 3 | Characterization of hepatitis B virus X gene quasispecies complexity in mono-infection and hepatitis delta virus superinfection显示文摘Hepatitis delta virus(HDV) seems to strongly suppress hepatitis B virus(HBV)replication, although little is known about the mechanism of this interaction. Both these viruses show a dynamic distribution of mutants, resulting in viral quasispecies. Next-generation sequencing is a viable approach for analyzing the composition of these mutant spectra. As the regulatory hepatitis B X protein(HBx) is essential for HBV replication, determination of HBV X gene(HBX)quasispecies complexity in HBV/HDV infection compared to HBV monoinfection may provide information on the interactions between these two viruses.AIM To compare HBV quasispecies complexity in the HBX 5' region between chronic hepatitis delta(CHD) and chronic HBV mono-infected patients.METHODS Twenty-four untreated patients were included: 7/24(29.2%) with HBeAgnegative chronic HBV infection(CI, previously termed inactive carriers), 8/24(33.3%) with HBeAg-negative chronic hepatitis B(CHB) and 9/24(37.5%) with CHD. A serum sample from each patient was first tested for HBV DNA levels.The HBX 5' region [nucleotides(nt) 1255-1611] was then PCR-amplified for subsequent next-generation sequencing(MiSeq, Illumina, United States). HBV quasispecies complexity in the region analyzed was evaluated using incidencebased indices(number of haplotypes and number of mutations), abundancebased indices(Hill numbers of order 1 and 2), and functional indices(mutation frequency and nucleotide diversity). We also evaluated the pattern of nucleotide changes to investigate which of them could be the cause of the quasispecies complexity.RESULTS CHB patients showed higher median HBV-DNA levels [5.4 logIU/mL,interquartile range(IQR) 3.5-7.9] than CHD(3.4 logIU/mL, IQR 3-7.6)(P = n.s.)or CI(3.2 logIU/mL, IQR 2.3-3.5)(P < 0.01) patients. The incidence and abundance indices indicated that HBV quasispecies complexity was significantly greater in CI than CHB. A similar trend was observed in CHD patients, although only Hill numbers of order 2 showed statistically significant differences(CHB2.81, IQR 1.11-4.57 vs CHD 8.87, 6.56-11.18, P = 0.038). There were no significant differences in the functional indices, but CI and CHD patients also showed a trend towards greater complexity than CHB. No differences were found for any HBV quasispecies complexity indices between CHD and CI patients. G-to-A and C-to-T nucleotide changes, characteristic of APOBEC3 G, were higher in CHD and CI than in CHB in genotype A haplotypes, but not in genotype D. The proportion of nt G-to-A vs A-to-G changes and C-to-T vs T-to-C changes in genotype A and D haplotypes in CHD patients showed no significant differences. In CHB and CI the results of these comparisons were dependent on HBV genotype.CONCLUSION The lower-replication CHD and CI groups show a trend to higher quasispecies complexity than the higher-replication CHB group. The mechanisms associated with this greater complexity require elucidation. | Cristina Godoy David Tabernero Sara Sopena Josep Gregori Maria Francesca Cortese Carolina González Rosario Casillas Mar?al Yll Ariadna Rando Rosa López-Martínez Josep Quer Gloria González-Aseguinolaza Rafael Esteban Mar Riveiro-Barciela Maria Buti Francisco Rodríguez-Frías | 2019 | World Journal of Gastroenterology2019，25，13： | 6 |
| 4 | Detection of hyper-conserved regions in hepatitis B virus X gene potentially useful for gene therapy显示文摘AIM To detect hyper-conserved regions in the hepatitis B virus(HBV) X gene(HBX) 5' region that could be candidates for gene therapy.METHODS The study included 27 chronic hepatitis B treatmentnaive patients in various clinical stages(from chronic infection to cirrhosis and hepatocellular carcinoma, both HBeA g-negative and HBeA g-positive), and infected with HBV genotypes A-F and H. In a serum sample from each patient with viremia > 3.5 log IU/m L, the HBX 5' end region [nucleotide(nt) 1255-1611] was PCRamplified and submitted to next-generation sequencing(NGS). We assessed genotype variants by phylogenetic analysis, and evaluated conservation of this region by calculating the information content of each nucleotide position in a multiple alignment of all unique sequences(haplotypes) obtained by NGS. Conservation at the HBx protein amino acid(aa) level was also analyzed.RESULTS NGS yielded 1333069 sequences from the 27 samples, with a median of 4578 sequences/sample(2487-9279, IQR 2817). In 14/27 patients(51.8%), phylogenetic analysis of viral nucleotide haplotypes showed a complex mixture of genotypic variants. Analysis of the information content in the haplotype multiple alignments detected 2 hyper-conserved nucleotide regions, one in the HBX upstream non-coding region(nt 1255-1286) and the other in the 5' end coding region(nt 1519-1603). This last region coded for a conserved amino acid region(aa 63-76) that partially overlaps a Kunitz-like domain.CONCLUSION Two hyper-conserved regions detected in the HBX 5' end may be of value for targeted gene therapy, regardless of the patients' clinical stage or HBV genotype. | Carolina González David Tabernero Maria Francesca Cortese Josep Gregori Rosario Casillas Mar Riveiro-Barciela Cristina Godoy Sara Sopena Ariadna Rando Marcal Yll Rosa Lopez-Martinez Josep Quer Rafael Esteban Maria Buti Francisco Rodríguez-Frías | 2018 | World Journal of Gastroenterology2018，24，19： | 6 |
| 5 | Quasispecies dynamics in main core epitopes of hepatitis B virus by ultra-deep-pyrosequencing显示文摘AIM:To investigate the variability of the main immunodominant motifs of hepatitis B virus(HBV) core gene by ultra-deep-pyrosequencing(UDPS).METHODS:Four samples(2 genotype A and 2 genotype D) from 4 treatment-na ve patients were assessed for baseline variability.Two additional samples from one patient(patient 4,genotype D) were selected for analysis:one sample corresponded to a 36-mo treatment-free period from baseline and the other to the time of viral breakthrough after 18 mo of lamivudine treatment.The HBV region analyzed covered amino acids 40 to 95 of the core gene,and included the two main epitopic regions,Th50-69 and B74-84.UDPS was carried out in the Genome Sequencer FLX system(454 Life Sciences,Roche).After computer filtering of UDPS data based on a Poisson statistical model,122 813 sequences were analyzed.The most conserved position detected by UDPS was analyzed by site-directed mutagenesis and evaluated in cell culture.RESULTS:Positions with highest variability rates were mainly located in the main core epitopes,confirming their role as immune-stimulating regions.In addition,the distribution of variability showed a relationship with HBV genotype.Patient 1(genotype A) presented the lowest variability rates and patient 2(genotype A) had 3 codons with variability higher than 1%.Patient 3 and 4(both genotype D) presented 5 and 8 codons with variability higher than 1%,respectively.The median baseline frequencies showed that genotype A samples had higher variability in epitopic positions than in the other positions analyzed,approaching significance(P = 0.07,sample 1 and P = 0.05,sample 2).In contrast,there were no significant differences in variability between the epitopic and other positions in genotype D cases.Interestingly,patient 1 presented a completely mutated motif from amino acid 64 to 67(E 64 LMT 67),which is commonly recognized by T helper cells.Additionally,the variability observed in all 4 patients was particularly associated with the E 64 LMT 67 motif.Codons 78 and 79 were highly conserved in all samples,in keeping with their involvement in the interaction between the HBV virion capsid and the surface antigens(HBsAg).Of note,codon 76 was even more conserved than codons 78 and 79,suggesting a possible role in HBsAg interactions or even in hepatitis B e antigen conformation.Sequential analysis of samples from patient 4(genotype D) illustrated the dynamism of the HBV quasispecies,with strong selection of one minor baseline variant coinciding with a decrease in core variability during the treatment-free and lamivudinetreated period.The drop in variability seemed to result from a 'steady state' situation of the HBV quasispecies after selection of the variant with greatest fitness.CONCLUSION:Host immune pressure seems to be the main cause of HBV core evolution.UDPS analysis is a useful technique for studying viral quasispecies. | Maria Homs Maria Buti David Tabernero Josep Quer Alex Sanchez Noelia Corral Rafael Esteban Francisco Rodriguez-Frias | 2012 | World Journal of Gastroenterology2012，18，42： | 5 |
| 6 | Analysis of hepatitis B virus preS1 variability and prevalence of the rs2296651 polymorphism in a Spanish population显示文摘AIM To determine the variability/conservation of the domain of hepatitis B virus(HBV) pre S1 region that interacts with sodium-taurocholate cotransporting polypeptide(hereafter, NTCP-interacting domain) and the prevalence of the rs2296651 polymorphism(S267 F, NTCP variant) in a Spanish population. METHODS Serum samples from 246 individuals were included and divided into 3 groups: patients with chronic HBV infection(CHB)(n = 41, 73% Caucasians), patients with resolved HBV infection(n = 100, 100% Caucasians) and an HBV-uninfected control group(n = 105, 100% Caucasians). Variability/conservation of the amino acid(aa) sequences of the NTCPinteracting domain,(aa 2-48 in viral genotype D) and a highly conserved pre S1 domain associated with virion morphogenesis(aa 92-103 in viral genotype D) were analyzed by next-generation sequencing and compared in 18 CHB patients with viremia > 4 log IU/mL. The rs2296651 polymorphism was determined in all individuals in all 3 groups using an in-house real-time PCR melting curve analysis.RESULTS The HBV pre S1 NTCP-interacting domain showed a high degree of conservation among the examined viral genomes especially between aa 9 and 21(in the genotype D consensus sequence). As compared with the virion morphogenesis domain, the NTCPinteracting domain had a smaller proportion of HBV genotype-unrelated changes comprising > 1% of the quasispecies(25.5% vs 31.8%), but a larger proportion of genotype-associated viral polymorphisms(34% vs 27.3%), according to consensus sequences from Gen Bank patterns of HBV genotypes A to H. Variation/conservation in both domains depended on viral genotype, with genotype C being the most highly conserved and genotype E the most variable(limited finding, only 2 genotype E included). Of note, proline residues were highly conserved in both domains, and serine residues showed changes only to threonine or tyrosine in the virion morphogenesis domain. The rs2296651 polymorphism was not detected in any participant.CONCLUSION In our CHB population, the NTCP-interacting domain was highly conserved, particularly the proline residues and essential amino acids related with the NTCP interaction, and the prevalence of rs2296651 was low/null. | Rosario Casillas David Tabernero Josep Gregori Irene Belmonte Maria Francesca Cortese Carolina González Mar Riveiro-Barciela Rosa Maria López Josep Quer Rafael Esteban Maria Buti Francisco Rodríguez-Frías | 2018 | World Journal of Gastroenterology2018，24，6： | 5 |
| 7 | Phase II Study of Everolimus in Patients with Metastatic Colorectal Adenocarcinoma Previously Treated with Bevacizumab-, Fluoropyrimidine-, Oxaliplatin-, and Irinotecan-Based Regimens显示文摘 | Kimmie Ng Josep Tabernero Jimmy Hwang Emilio Bajetta Sunil Sharma Salvatore A. Del Prete Edward R. Arrowsmith David P. Ryan Michaela Sedova Jin Jin Kamel Malek Charles S. Fuchs | 2013 | Clinical Cancer Research2013，，14： | 4 |
| 8 | Bevacizumab plus oxaliplatin-based chemotherapy as adjuvant treatment for colon cancer (AVANT): a phase 3 randomised controlled trial显示文摘 | Aimery de Gramont Eric Van Cutsem Hans-Joachim Schmoll Josep Tabernero Stephen Clarke Malcolm J Moore David Cunningham Thomas H Cartwright J Randolph Hecht Fernando Rivera Seock-Ah Im Gy?rgy Bodoky Ramon Salazar Frédérique Maindrault-Goebel Einat Shacham- | 2012 | Lancet Oncology2012，，12： | 3 |
| 9 | Development of Molecular Biomarkers in Individualized Treatment of Colorectal Cancer显示文摘 | Leticia De Mattos-Arruda Rodrigo Dienstmann Josep Tabernero | 2011 | Clinical Colorectal Cancer2011，，4： | 2 |
| 10 | EGFR and KRAS in Colorectal Cancer显示文摘 | Ben Markman Francisco Javier Ramos Jaume Capdevila Josep Tabernero | 2010 | Advances in Clinical Chemistry2010，，： | 2 |
| 11 | Phase Ⅲ trial of capecitabine plus oxaliplatin as adjuvant therapy for stage Ⅲ colon cancer:a planned safety analysis in 1864 patients显示文摘 | Schmoll HJ Cartwright T Tabernero J | | Journal of Clinical Oncology0，，： | 2 |
| 12 | Adult precursor BALL with BCR/ABL gene rearrangements displays a unique immunophenotype based on the patten, of CD10, CD34, CD13 and CD38 expression 显示文摘 | Tabernero MD Bortoluci AM Alaejos I | 2001 | Leukemia2001，15，3： | 1 |
| 13 | Effects of grape antioxidant dietary fiber in cardiovascular disease risk factors显示文摘 | Pérez-Jiménez J Scrrano J Tabernero M | 2008 | Nutrition2008，，24： | 1 |
| 14 | XELOX (capecitabine plus oxaliplatin):active first-line therapy for patients with metastatic colorectal cancer显示文摘 | Cassidy J Tabernero J Twelves C | 2004 | J Clin Oncol2004，22，11： | 1 |
| 15 | XELOX (Capecitabine Plus Oxaliplatin):Active First-Line Therapy for Patients With Metastatic Colorectal Cancer显示文摘 | Cassidy J Tabernero J Twelves C | 2004 | J Clin Oncol2004，22，11： | 1 |
| 16 | Capecitabine plus OXALIPLATIN (XELOX): highly active , fine combination therapy for metastatic CRC 显示文摘 | Tabernero J | 2002 | Proc Am Soc Clin Oncol2002，21，： | 1 |
| 17 | PhaseⅡtrial of preoperative irinotecancisplatin followed by concurrent irinotecancisplatin and radio-therapy for respectable locally advanced gastric and esophagogastric junction adenocarcinoma显示文摘 | Rivera F Galán M Tabernero J | 2009 | Int J Radiat Oncol Biol Phys2009，75，5： | 1 |
| 18 | Xel ox(Capecitabine Plus Oxaliplatin):Active First -Line Therapy for Patients With Metastatic Colorectal Cancer显示文摘 | Cassidy J Tabernero J Twelves C | | 0，，11： | 1 |
| 19 | Xelox( capecitabine plus oxaliplatin) :active first-line therapy for patients with metastatic color- ectal cancer 显示文摘 | Cassidy J Tabernero J Twelves C | 2004 | J Clin Onco12004，22，11： | 1 |
| 20 | Peripheral refraction profiles in subjects with low foveal refractive errors显示文摘 | Tabernero J Ohlendorf A Fischer MD | | 0，，： | 1 |
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