Browsing by Author "Luo, W"

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Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project
(Taylor and Francis Ltd., 2024) Vale, FF; Roberts, RJ; Kobayashi, I; Camargo, MC; Rabkin, CS; Wang, D; Hicks, B; Zhu, B; Yeager, M; Hutchinson, A; Teshome, K; Jones, K; Luo, W; Goldstein, AM; Hu, N; Taylor, PR; Song, M; Gutiérrez-Escobar, AJ; Yu, K; Abnet, CC; Chanock, SJ; Romero-Gallo, J; Krishna, U; Peek, RM; Piazuelo, MB; Wilson, KT; Loh, JT; Cover, TL; Raaf, N; Aftab, H; Akada, J; Matsumoto, T; Yamaoka, Y; Haesebrouck, F; Bartelli, TF; Nunes, DN; Pelosof, A; Sztokfisz, CZ; Dias-Neto, E; Assumpção, PP; Tishkov, I; Goodman, KJ; Geary, J; Cromarty, TJ; Price, NL; Quilty, D; Corvalan, AH; Serrano, CA; Gonzalez, R; Riquelme, A; García-Cancino, A; Parra-Sepúlveda, C; Castillo, F; Bravo, MM; Pazos, A; Bravo, LE; Fox, JG; Ramírez-Mayorga, V; Molina-Castro, S; Durán-Bermúdez, S; Campos-Núñez, C; Chaves-Cervantes, M; Tshibangu-Kabamba, E; Tumba, GD; Tshimpi-Wola, A; de Jesus Ngoma-Kisoko, P; Ngoyi, DM; Cruz, M; Hosking, C; Abreu, JJ; Varon, C; Benejat, L; Jehanne, Q; Lehours, P; Megraud, F; Secka, O; Link, A; Malfertheiner, P; Adinortey, MB; Bockarie, AS; Adinortey, CA; Ofori, EG; Sgouras, DN; Martinez-Gonzalez, B; Michopoulos, S; Georgopoulos, S; Hernandez, E; Dominguez, RL; Morgan, DR; Harðardóttir, H; Gunnarsdóttir, AI; Guðjónsson, H; Jónasson, JG; Björnsson, ES; Ballal, M; Shetty, V; Miftahussurur, M; Sugihartono, T; Alfaray, RI; Waskito, LA; Fauzia, KA; Syam, AF; Maulahela, H; Malekzadeh, R; Sotoudeh, M; Peretz, A; Azrad, M; On, A; De, Re, V; Zanussi, S; Cannizzaro, R; Canzonieri, V; Shimura, T; Tokunaga, K; Osaki, T; Kamiya, S; Jadallah, K; Matalka, I; Sagynbekuly, IN; Moldobaeva, MS; Rakhat, A; Choi, IJ; Kim, JG; Kim, N; Leja, M; Vangravs, R; Šķenders, Ģ; Rūdule, A; Kikuste, I; Vanags, A; Rudzīte, D; Kupcinskas, J; Skieceviciene, J; Jonaitis, L; Kiudelis, G; Jonaitis, P; Kiudelis, V; Varkalaite, G; Vadivelu, J; Loke, MF; Vellasamy, KM; Herrera-Goepfert, R; Alonso-Larraga, JO; Yee, TT; Htet, K; Matsuhisa, T; Shrestha, PK; Ansari, S; Abiodun, O; Jemilohun, C; Akande, KO; Olu-Abiodun, O; Magaji, FA; Omotoso, A; Okonkwo, U; Osuagwu, CC; Owoseni, OO; Castaneda, C; Castillo, M; Velapatino, B; Gilman, RH; Krzyżek, P; Gościniak, G; Pawełka, D; Korona-Glowniak, I; Cichoz-Lach, H; Oleastro, M; Figueiredo, C; Machado, JC; Ferreira, RM; Bordin, DS; Livzan, MA; Tsukanov, VV; Tan, P; Yeoh, KG; Zhu, F; Ally, R; Haas, R; Fischer, W; Montes, M; Fernández-Reyes, M; Tamayo, E; Lizasoain, J; Bujanda, L; Lario, S; Ramírez-Lázaro, MJ; Calvet, X; Brunet-Mas, E; Domper-Arnal, MJ; García-Mateo, S; Abad-Baroja, D; Delgado-Guillena, P; Moreira, L; Botargues, J; Pérez-Martínez, I; Barreiro-Alonso, E; Flores, V; Gisbert, JP; Muro, EA; Linares, P; Alcoba, L; Martin, V; Fleitas-Kanonnikoff, T; Altayeb, HN; Engstrand, L; Enroth, H; Keller, PM; Wagner, K; Pohl, D; Lee, Y-C; Liou, J-M; Wu, M-S; Kocazeybek, B; Sarıbas, S; Tasçı, İ; Demiryas, S; Kepil, N; Quiel, L; Villagra, M; Norton, M; Johnson, D; Huang, RJ; Hwang, JH; Szymczak, W; Rajagopalan, S; Asare, E; Jacobs, WR; In, H; Bollag, R; Lopez, A; Kruse, EJ; White, J; Graham, DY; Lane, C; Gao, Y; Gold, BD; Cruz-Correa, M; González-Pons, M; Rodriguez, LM; Tuan, VP; Dung, HDQ; Binh, TT; Trang, TTH; Van, Khien, V; Chen, X; Zhao, Y; Raley, C; Kessing, B; Tran, B; Katsura, Y; Gonzalez-Hormazabal, P; Didelot, X; Sheppard, S; Tarazona-Santos, E; Zamudio, R; Mariño-Ramírez, L; Backert, S; Naumann, M; Smet, A; Berg, DE; Chiner-Oms, Á; Comas, I; Martínez-Martínez, FJ; Yahara, K; Blaser, MJ; Vincze, T; Morgan, RD; Dekker, JP; Torres, J; Noureen, M; Cherry, JL; Osada, N; Fukuyo, M; Arita, M; Sandoval-Motta, S; Agostini, RB; Ghirotto, S; Muñoz-Ramírez, ZY; Torres, RC; Falush, D; Thorell, K; Uchiyama, I
Prophages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of Helicobacter pylori, a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Helicobacter pylori Genome Project (HpGP) dataset comprises 1011 H. pylori complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the H. pylori prophage genomic content in the HpGP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29.5% (298) of the HpGP genomes contain prophages, of which only 32.2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of H. pylori prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in H. pylori. We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for H. pylori prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages. © 2024 The Author(s). Published with license by Taylor & Francis Group, LLC.
Treatment Efficacy, Adherence, and Quality of Life Among Women Younger Than 35 Years in the International Breast Cancer Study Group TEXT and SOFT Adjuvant Endocrine Therapy Trials
(American Society of Clinical Oncology, 2017) Saha, P; Regan, MM; Pagani, O; Francis, PA; Walley, BA; Ribi, K; Bernhard, J; Luo, W; Gómez, HL; Burstein, HJ; Parmar, V; Torres, R; Stewart, J; Bellet, M; Perelló, A; Dane, F; Moreira, A; Vorobiof, D; Nottage, M; Price, KN; Coates, AS; Goldhirsch, A; Gelber, RD; Colleoni, M; Fleming, GF; SOFT TEXT Investigators; International Breast Cancer Study Group
Purpose To describe benefits and toxicities of adjuvant endocrine therapies in women younger than 35 years with breast cancer (n = 582) enrolled in the Suppression of Ovarian Function Trial (SOFT) and Tamoxifen and Exemestane Trial (TEXT). Methods In SOFT, women still premenopausal after surgery with or without chemotherapy were randomly assigned to tamoxifen alone, tamoxifen plus ovarian function suppression (OFS), or exemestane plus OFS. In TEXT, all received OFS with or without concomitant chemotherapy and were randomly assigned to exemestane plus OFS or tamoxifen plus OFS. We summarize treatment efficacy, quality of life, and adherence of the cohort of women younger than 35 years in SOFT and TEXT, alongside data from the cohort of older premenopausal women. Results For 240 human epidermal growth factor receptor 2-negative patients younger than 35 years enrolled in SOFT after receiving chemotherapy, the 5-year breast cancer-free interval (BCFI) was 67.1% (95% CI, 54.6% to 76.9%) with tamoxifen alone, 75.9% with tamoxifen plus OFS (95% CI, 64.0% to 84.4%), and 83.2% with exemestane plus OFS (95% CI, 72.7% to 90.0%). For 145 human epidermal growth factor receptor 2-negative patients younger than 35 years in TEXT, 5-year BCFI was 79.2% (95% CI, 66.2% to 87.7%) with tamoxifen plus OFS and 81.6% (95% CI, 69.8% to 89.2%) with exemestane plus OFS. The most prominent quality of life symptom for patients younger than 35 years receiving OFS was vasomotor symptoms, with the greatest worsening from baseline at 6 months (on the order of 30 to 40 points), but loss of sexual interest and difficulties in becoming aroused were also clinically meaningful (≥ 8-point change). The level of symptom burden was similar in older premenopausal women. A total of 19.8% of women younger than 35 years stopped all protocol-assigned endocrine therapy early. Conclusion In women younger than 35 years with hormone receptor-positive breast cancer, adjuvant OFS combined with tamoxifen or exemestane produces large improvements in BCFI compared with tamoxifen alone. Menopausal symptoms are significant but are not worse than those seen in older premenopausal women.