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1,016 results on '"Hoshida, Yujin"'

2. An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection

Author

Mukherji, Atish, Jühling, Frank, Simanjuntak, Yogy, Crouchet, Emilie, Del Zompo, Fabio, Teraoka, Yuji, Haller, Alexandre, Baltzinger, Philippe, Paritala, Soumith, Rasha, Fahmida, Fujiwara, Naoto, Gadenne, Cloé, Slovic, Nevena, Oudot, Marine A., Durand, Sarah C., Ponsolles, Clara, Schuster, Catherine, Zhuang, Xiaodong, Holmes, Jacinta, Yeh, Ming-Lun, Abe-Chayama, Hiromi, Heikenwälder, Mathias, Sangiovanni, Angelo, Iavarone, Massimo, Colombo, Massimo, Foung, Steven K. H., McKeating, Jane A., Davidson, Irwin, Yu, Ming-Lung, Chung, Raymond T., Hoshida, Yujin, Chayama, Kazuaki, Lupberger, Joachim, and Baumert, Thomas F.

Published
2024
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3. The phosphatidylserine targeting antibody bavituximab plus pembrolizumab in unresectable hepatocellular carcinoma: a phase 2 trial

Author

Hsiehchen, David, Beg, Muhammad S., Kainthla, Radhika, Lohrey, Jay, Kazmi, Syed M., Khosama, Leticia, Maxwell, Mary Claire, Kline, Heather, Katz, Courtney, Hassan, Asim, Kubota, Naoto, Siglinsky, Ellen, Pillai, Anil K., Youssoufian, Hagop, Mockbee, Colleen, Culm, Kerry, Uhlik, Mark, Benjamin, Laura, Brekken, Rolf A., Ahn, Chul, Singal, Amit G., Zhu, Hao, Hoshida, Yujin, and Yopp, Adam C.

Published
2024
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5. A multi‐analyte cell‐free DNA–based blood test for early detection of hepatocellular carcinoma

Author

Lin, Nan, Lin, Yongping, Xu, Jianfeng, Liu, Dan, Li, Diange, Meng, Hongyu, Gallant, Maxime A, Kubota, Naoto, Roy, Dhruvajyoti, Li, Jason S, Gorospe, Emmanuel C, Sherman, Morris, Gish, Robert G, Abou‐Alfa, Ghassan K, Nguyen, Mindie H, Taggart, David J, Van Etten, Richard A, Hoshida, Yujin, and Li, Wei

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Digestive Diseases, Rare Diseases, Cancer, Genetics, Prevention, Clinical Research, Liver Disease, Liver Cancer, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, 4.2 Evaluation of markers and technologies, Good Health and Well Being, Carcinoma, Hepatocellular, Cell-Free Nucleic Acids, Early Detection of Cancer, Hematologic Tests, Humans, Liver Neoplasms, Prospective Studies, alpha-Fetoproteins, Clinical sciences
Abstract

The limited performance of guideline-recommended abdominal ultrasound and serum alpha-fetoprotein (AFP) highlights the urgent, unmet need for new biomarkers for more accurate detection of early hepatocellular carcinoma (HCC). To this end, we have conducted a prospective clinical validation study to evaluate the performance of the HelioLiver Test, a multi-analyte blood test combining cell-free DNA methylation patterns, clinical variables, and protein tumor markers. A blinded, multicenter validation study was performed with 247 subjects, including 122 subjects with HCC and 125 control subjects with chronic liver disease. The performance of the HelioLiver Test was compared with AFP and the GALAD score as established HCC surveillance blood tests. The performance of the HelioLiver Test (area under the receiver operating characteristic curve [AUROC] = 0.944) was superior to both AFP (AUROC = 0.851; p < 0.0001) and GALAD (AUROC = 0.899; p < 0.0001). Using a prespecified diagnostic algorithm, the HelioLiver Test showed sensitivities of 85% (95% confidence interval [CI], 78%-90%) for HCC of any stage and 76% (95% CI, 60%-87%) for early stage (American Joint Committee on Cancer [AJCC] I and II) HCC. In contrast, AFP (≥20 ng/mL) alone and the GALAD score (≥-0.63) showed lower sensitivities of 62% (95% CI, 54%-70%) and 75% (95% CI, 67%-82%) for HCC overall, and 57% (95% CI, 40%-71%) and 65% (95% CI, 49%-79%) for early stage (AJCC I and II) HCC, respectively. The specificities of the HelioLiver Test (91%; 95% CI, 85%-95%), AFP (97%; 95% CI, 92%-99%), and the GALAD score (94%; 95% CI, 88%-97%) were similar for control subjects. The HelioLiver Test showed superior performance for HCC detection compared to with both AFP and the GALAD score and warrants further evaluation in HCC surveillance settings.

Published
2022

13. Opposing roles of hepatic stellate cell subpopulations in hepatocarcinogenesis

Author

Filliol, Aveline, Saito, Yoshinobu, Nair, Ajay, Dapito, Dianne H., Yu, Le-Xing, Ravichandra, Aashreya, Bhattacharjee, Sonakshi, Affo, Silvia, Fujiwara, Naoto, Su, Hua, Sun, Qiuyan, Savage, Thomas M., Wilson-Kanamori, John R., Caviglia, Jorge M., Chin, LiKang, Chen, Dongning, Wang, Xiaobo, Caruso, Stefano, Kang, Jin Ku, Amin, Amit Dipak, Wallace, Sebastian, Dobie, Ross, Yin, Deqi, Rodriguez-Fiallos, Oscar M., Yin, Chuan, Mehal, Adam, Izar, Benjamin, Friedman, Richard A., Wells, Rebecca G., Pajvani, Utpal B., Hoshida, Yujin, Remotti, Helen E., Arpaia, Nicholas, Zucman-Rossi, Jessica, Karin, Michael, Henderson, Neil C., Tabas, Ira, and Schwabe, Robert F.

Published
2022
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15. Treatment of HCC with claudin-1-specific antibodies suppresses carcinogenic signaling and reprograms the tumor microenvironment

Author

Roehlen, Natascha, Muller, Marion, Nehme, Zeina, Crouchet, Emilie, Jühling, Frank, Del Zompo, Fabio, Cherradi, Sara, Duong, Francois H.T., Almeida, Nuno, Saviano, Antonio, Fernández-Vaquero, Mirian, Riedl, Tobias, El Saghire, Houssein, Durand, Sarah C., Ponsolles, Clara, Oudot, Marine A., Martin, Romain, Brignon, Nicolas, Felli, Emanuele, Pessaux, Patrick, Lallement, Antonin, Davidson, Irwin, Bandiera, Simonetta, Thumann, Christine, Marchand, Patrice, Moll, Solange, Nicolay, Brandon, Bardeesy, Nabeel, Hoshida, Yujin, Heikenwälder, Mathias, Iacone, Roberto, Toso, Alberto, Meyer, Markus, Elson, Greg, Schweighoffer, Tamas, Teixeira, Geoffrey, Zeisel, Mirjam B., Laquerriere, Patrice, Lupberger, Joachim, Schuster, Catherine, Mailly, Laurent, and Baumert, Thomas F.

Published
2023
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16. Recent Developments and Therapeutic Strategies against Hepatocellular Carcinoma

Author

Yarchoan, Mark, Agarwal, Parul, Villanueva, Augusto, Rao, Shuyun, Dawson, Laura A, Karasic, Thomas, Llovet, Josep M, Finn, Richard S, Groopman, John D, El-Serag, Hashem B, Monga, Satdarshan P, Wang, Xin Wei, Karin, Michael, Schwartz, Robert E, Tanabe, Kenneth K, Roberts, Lewis R, Gunaratne, Preethi H, Tsung, Allan, Brown, Kimberly A, Lawrence, Theodore S, Salem, Riad, Singal, Amit G, Kim, Amy K, Rabiee, Atoosa, Resar, Linda, Meyer, Jeffrey, Hoshida, Yujin, He, Aiwu Ruth, Ghoshal, Kalpana, Ryan, Patrick B, Jaffee, Elizabeth M, Guha, Chandan, Mishra, Lopa, Coleman, C Norman, and Ahmed, Mansoor M

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Digestive Diseases, Liver Disease, Liver Cancer, Cancer, Orphan Drug, Rare Diseases, Chronic Liver Disease and Cirrhosis, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Anilides, Antibodies, Monoclonal, Humanized, Carcinoma, Hepatocellular, Chemoembolization, Therapeutic, Clinical Trials as Topic, Humans, Immunotherapy, Liver Neoplasms, Molecular Targeted Therapy, Mutation, Phenylurea Compounds, Protein Kinase Inhibitors, Pyridines, Quinolines, beta Catenin, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Hepatocellular carcinoma (HCC) has emerged as a major cause of cancer deaths globally. The landscape of systemic therapy has recently changed, with six additional systemic agents either approved or awaiting approval for advanced stage HCC. While these agents have the potential to improve outcomes, a survival increase of 2-5 months remains poor and falls short of what has been achieved in many other solid tumor types. The roles of genomics, underlying cirrhosis, and optimal use of treatment strategies that include radiation, liver transplantation, and surgery remain unanswered. Here, we discuss new treatment opportunities, controversies, and future directions in managing HCC.

Published
2019

18. High Neutrophil–Lymphocyte Ratio and Delta Neutrophil–Lymphocyte Ratio Are Associated with Increased Mortality in Patients with Hepatocellular Cancer

Author

Rich, Nicole E., Parvathaneni, Aarthi, Sen, Ahana, Odewole, Mobolaji, Arroyo, Ana, Mufti, Arjmand R., Kerr, Thomas A., Grant, Lafaine, Tujios, Shannan R., Mayo, Marlyn J., Lee, William M., Yang, Ju Dong, Yokoo, Takeshi, Gopal, Purva, Hoshida, Yujin, Zhu, Hao, Yopp, Adam C., Marrero, Jorge A., and Singal, Amit G.

Published
2022
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21. Peroxidasin Deficiency Re-programs Macrophages Toward Pro-fibrolysis Function and Promotes Collagen Resolution in Liver

Author

Sojoodi, Mozhdeh, Erstad, Derek J., Barrett, Stephen C., Salloum, Shadi, Zhu, Shijia, Qian, Tongqi, Colon, Selene, Gale, Eric M., Jordan, Veronica Clavijo, Wang, Yongtao, Li, Shen, Ataeinia, Bahar, Jalilifiroozinezhad, Sasan, Lanuti, Michael, Zukerberg, Lawrence, Caravan, Peter, Hoshida, Yujin, Chung, Raymond T., Bhave, Gautam, Lauer, Georg M., Fuchs, Bryan C., and Tanabe, Kenneth K.

Published
2022
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22. Stromal and Immune Drivers of Hepatocarcinogenesis

Author

Saviano, Antonio, Roehlen, Natascha, Virzì, Alessia, Roca Suarez, Armando Andres, Hoshida, Yujin, Lupberger, Joachim, Baumert, Thomas F., Coleman, William B., Series Editor, Tsongalis, Gregory J., Series Editor, and Hoshida, Yujin, editor

Published
2019
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24. OS-061 Chronic hepatitis C virus infection induces HCC risk by perturbing the human liver circadian transcriptome and epigenome through deregulation of the deacetylase SIRT1

Author

Mukherji, Atish, primary, Jühling, Frank, additional, Simanjuntak, Yogy, additional, Imamura, Michio, additional, Crouchet, Emilie, additional, Del Zompo, Fabio, additional, Teraoka, Yuji, additional, Haller, Alexandre, additional, Baltzinger, Philippe, additional, Paritala, Soumith, additional, Rasha, Fahmida, additional, Fujiwara, Naoto, additional, Gadenne, Cloé, additional, Slovic, Nevena, additional, Oudot, Marine, additional, Durand, Sarah, additional, Ponsolles, Clara, additional, Schuster, Catherine, additional, Zhuang, Xiaodong, additional, Holmes, Jacinta, additional, Yeh, Ming-Lun, additional, Abe-Chayama, Hiromi, additional, Heikenwälder, Mathias, additional, Sangiovanni, Angelo, additional, Iavarone, Massimo, additional, Colombo, Massimo, additional, McKeating, Jane, additional, Davidson, Irwin, additional, Yu, Ming-Lung, additional, Chung, Raymond, additional, Hoshida, Yujin, additional, Chayama, Kazuaki, additional, Lupberger, Joachim, additional, and Baumert, Thomas, additional

Published
2024
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25. OS-013 Targeting the histamine receptor 2 for HCC chemoprevention

Author

Crouchet, Emilie, primary, Katz, Courtney, additional, Fujiwara, Naoto, additional, Jühling, Frank, additional, Oudot, Marine, additional, Durand, Sarah, additional, Saviano, Antonio, additional, Martin, Romain, additional, Giannone, Fabio, additional, Pessaux, Patrick, additional, Chung, Raymond, additional, Schuster, Catherine, additional, Mailly, Laurent, additional, Hoshida, Yujin, additional, and Baumert, Thomas, additional

Published
2024
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26. A blood-based prognostic liver secretome signature and long-term hepatocellular carcinoma risk in advanced liver fibrosis

Author

Fujiwara, Naoto, Kobayashi, Masahiro, Fobar, Austin J., Hoshida, Ayaka, Marquez, Cesia A., Koneru, Bhuvaneswari, Panda, Gayatri, Taguri, Masataka, Qian, Tongqi, Raman, Indu, Li, Quan-Zhen, Hoshida, Hiroki, Sezaki, Hitomi, Kumada, Hiromitsu, Tateishi, Ryosuke, Yokoo, Takeshi, Yopp, Adam C., Chung, Raymond T., Fuchs, Bryan C., Baumert, Thomas F., Marrero, Jorge A., Parikh, Neehar D., Zhu, Shijia, Singal, Amit G., and Hoshida, Yujin

Published
2021
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28. The Spatial Extracellular Proteomic Tumor Microenvironment Distinguishes Molecular Subtypes of Hepatocellular Carcinoma.

Author

Macdonald, Jade K., Taylor, Harrison B., Wang, Mengjun, Delacourt, Andrew, Edge, Christin, Lewin, David N., Kubota, Naoto, Fujiwara, Naoto, Rasha, Fahmida, Marquez, Cesia A., Ono, Atsushi, Oka, Shiro, Chayama, Kazuaki, Lewis, Sara, Taouli, Bachir, Schwartz, Myron, Fiel, M Isabel, Drake, Richard R., Hoshida, Yujin, and Mehta, Anand S.

Published
2024
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31. Aspirin for Metabolic Dysfunction–Associated Steatotic Liver Disease Without Cirrhosis

Author

Simon, Tracey G., primary, Wilechansky, Robert M., additional, Stoyanova, Stefania, additional, Grossman, Alessandra, additional, Dichtel, Laura E., additional, Lauer, Georg M., additional, Miller, Karen K., additional, Hoshida, Yujin, additional, Corey, Kathleen E., additional, Loomba, Rohit, additional, Chung, Raymond T., additional, and Chan, Andrew T., additional

Published
2024
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34. Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma

Author

Finkin, Shlomi, Yuan, Detian, Stein, Ilan, Taniguchi, Koji, Weber, Achim, Unger, Kristian, Browning, Jeffrey L, Goossens, Nicolas, Nakagawa, Shigeki, Gunasekaran, Ganesh, Schwartz, Myron E, Kobayashi, Masahiro, Kumada, Hiromitsu, Berger, Michael, Pappo, Orit, Rajewsky, Klaus, Hoshida, Yujin, Karin, Michael, Heikenwalder, Mathias, Ben-Neriah, Yinon, and Pikarsky, Eli

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Liver Disease, Rare Diseases, Liver Cancer, Cancer, Stem Cell Research, Digestive Diseases, 2.1 Biological and endogenous factors, Aetiology, Adaptive Immunity, Animals, Carcinoma, Hepatocellular, Comparative Genomic Hybridization, Cytokines, Disease Models, Animal, Hepatocytes, Humans, I-kappa B Kinase, Immunity, Innate, Immunoblotting, In Situ Hybridization, Liver Neoplasms, Lymphoid Tissue, Mice, Inbred C57BL, Mice, Knockout, Mice, Transgenic, NF-kappa B, Neoplastic Stem Cells, Reverse Transcriptase Polymerase Chain Reaction, Stem Cell Niche, T-Lymphocytes, Transcriptome, Biochemistry and cell biology
Abstract

Ectopic lymphoid-like structures (ELSs) are often observed in cancer, yet their function is obscure. Although ELSs signify good prognosis in certain malignancies, we found that hepatic ELSs indicated poor prognosis for hepatocellular carcinoma (HCC). We studied an HCC mouse model that displayed abundant ELSs and found that they constituted immunopathological microniches wherein malignant hepatocyte progenitor cells appeared and thrived in a complex cellular and cytokine milieu until gaining self-sufficiency. The egress of progenitor cells and tumor formation were associated with the autocrine production of cytokines previously provided by the niche. ELSs developed via cooperation between the innate immune system and adaptive immune system, an event facilitated by activation of the transcription factor NF-κB and abolished by depletion of T cells. Such aberrant immunological foci might represent new targets for cancer therapy.

Published
2015

35. A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery

Author

Crouchet, Emilie, Bandiera, Simonetta, Fujiwara, Naoto, Li, Shen, El Saghire, Hussein, Fernández-Vaquero, Mirian, Riedl, Tobias, Sun, Xiaochen, Hirschfield, Hadassa, Jühling, Frank, Zhu, Shijia, Roehlen, Natascha, Ponsolles, Clara, Heydmann, Laura, Saviano, Antonio, Qian, Tongqi, Venkatesh, Anu, Lupberger, Joachim, Verrier, Eloi R., Sojoodi, Mozhdeh, Oudot, Marine A., Duong, François H. T., Masia, Ricard, Wei, Lan, Thumann, Christine, Durand, Sarah C., González-Motos, Victor, Heide, Danijela, Hetzer, Jenny, Nakagawa, Shigeki, Ono, Atsushi, Song, Won-Min, Higashi, Takaaki, Sanchez, Roberto, Kim, Rosa S., Bian, C. Billie, Kiani, Karun, Croonenborghs, Tom, Subramanian, Aravind, Chung, Raymond T., Straub, Beate K., Schuppan, Detlef, Ankavay, Maliki, Cocquerel, Laurence, Schaeffer, Evelyne, Goossens, Nicolas, Koh, Anna P., Mahajan, Milind, Nair, Venugopalan D., Gunasekaran, Ganesh, Schwartz, Myron E., Bardeesy, Nabeel, Shalek, Alex K., Rozenblatt-Rosen, Orit, Regev, Aviv, Felli, Emanuele, Pessaux, Patrick, Tanabe, Kenneth K., Heikenwälder, Mathias, Schuster, Catherine, Pochet, Nathalie, Zeisel, Mirjam B., Fuchs, Bryan C., Hoshida, Yujin, and Baumert, Thomas F.

Published
2021
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37. Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of Hepatitis C Virus–Infected Cells and Liver to Identify Pathways Associated With Disease Development

Author

Lupberger, Joachim, Croonenborghs, Tom, Roca Suarez, Armando Andres, Van Renne, Nicolaas, Jühling, Frank, Oudot, Marine A., Virzì, Alessia, Bandiera, Simonetta, Jamey, Carole, Meszaros, Gergö, Brumaru, Daniel, Mukherji, Atish, Durand, Sarah C., Heydmann, Laura, Verrier, Eloi R., El Saghire, Hussein, Hamdane, Nourdine, Bartenschlager, Ralf, Fereshetian, Shaunt, Ramberger, Evelyn, Sinha, Rileen, Nabian, Mohsen, Everaert, Celine, Jovanovic, Marko, Mertins, Philipp, Carr, Steven A., Chayama, Kazuaki, Dali-Youcef, Nassim, Ricci, Romeo, Bardeesy, Nabeel M., Fujiwara, Naoto, Gevaert, Olivier, Zeisel, Mirjam B., Hoshida, Yujin, Pochet, Nathalie, and Baumert, Thomas F.

Published
2019
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39. Inhibiting SCAP/SREBP exacerbates liver injury and carcinogenesis in murine nonalcoholic steatohepatitis

Author

Kawamura, Satoshi, Matsushita, Yuki, Kurosaki, Shigeyuki, Tange, Mizuki, Fujiwara, Naoto, Hayata, Yuki, Hayakawa, Yoku, Suzuki, Nobumi, Hata, Masahiro, Tsuboi, Mayo, Kishikawa, Takahiro, Kinoshita, Hiroto, Nakatsuka, Takuma, Sato, Masaya, Kudo, Yotaro, Hoshida, Yujin, Umemura, Atsushi, Eguchi, Akiko, Ikenoue, Tsuneo, Hirata, Yoshihiro, Uesugi, Motonari, Tateishi, Ryosuke, Tateishi, Keisuke, Fujishiro, Mitsuhiro, Koike, Kazuhiko, and Nakagawa, Hayato

Subjects
Binding proteins -- Physiological aspects -- Health aspects, Fatty acids -- Synthesis, Fatty liver -- Development and progression -- Care and treatment, Health care industry
Abstract

Enhanced de novo lipogenesis mediated by sterol regulatory element-binding proteins (SREBPs) is thought to be involved in nonalcoholic steatohepatitis (NASH) pathogenesis. In this study, we assessed the impact of SREBP inhibition on NASH and liver cancer development in murine models. Unexpectedly, SREBP inhibition via deletion of the SREBP cleavage-activating protein (SCAP) in the liver exacerbated liver injury, fibrosis, and carcinogenesis despite markedly reduced hepatic steatosis. These phenotypes were ameliorated by restoring SREBP function. Transcriptome and lipidome analyses revealed that SCAP/SREBP pathway inhibition altered the fatty acid (FA) composition of phosphatidylcholines due to both impaired FA synthesis and disorganized FA incorporation into phosphatidylcholine via lysophosphatidylcholine acyltransferase 3 (LPCAT3) downregulation, which led to endoplasmic reticulum (ER) stress and hepatocyte injury. Supplementation with phosphatidylcholines significantly improved liver injury and ER stress induced by SCAP deletion. The activity of the SCAP/ SREBP/LPCAT3 axis was found to be inversely associated with liver fibrosis severity in human NASH. SREBP inhibition also cooperated with impaired autophagy to trigger liver injury. Thus, excessively strong and broad lipogenesis inhibition was counterproductive for NASH therapy; this will have important clinical implications in NASH treatment., Introduction Nonalcoholic steatohepatitis (NASH) is a severe form of nonalcoholic fatty liver disease (NAFLD) that is characterized by hepatic steatosis, inflammation, hepatocellular injury, and fibrosis, which lead to progression of [...]

Published
2022
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41. Combination of Gene Expression Signature and Model for End-Stage Liver Disease Score Predicts Survival of Patients With Severe Alcoholic Hepatitis

Author

Trépo, Eric, Goossens, Nicolas, Fujiwara, Naoto, Song, Won-Min, Colaprico, Antonio, Marot, Astrid, Spahr, Laurent, Demetter, Pieter, Sempoux, Christine, Im, Gene Y., Saldarriaga, Joan, Gustot, Thierry, Devière, Jacques, Thung, Swan N., Minsart, Charlotte, Sersté, Thomas, Bontempi, Gianluca, Abdelrahman, Karim, Henrion, Jean, Degré, Delphine, Lucidi, Valerio, Rubbia-Brandt, Laura, Nair, Venugopalan D., Moreno, Christophe, Deltenre, Pierre, Hoshida, Yujin, and Franchimont, Denis

Published
2018
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42. Cell type-specific pharmacological kinase inhibition for cancer chemoprevention

Author

Deshmukh, Manjeet, Nakagawa, Shigeki, Higashi, Takaaki, Vincek, Adam, Venkatesh, Anu, Ruiz de Galarreta, Marina, Koh, Anna P, Goossens, Nicolas, Hirschfield, Hadassa, Bian, C Billie, Fujiwara, Naoto, Ono, Atsushi, Hoshida, Hiroki, El-Abtah, Mohamed, Ahmad, Noor B, Lujambio, Amaia, Sanchez, Roberto, Fuchs, Bryan C, Poelstra, Klaas, Prakash, Jai, and Hoshida, Yujin

Published
2018
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45. Master Transcription Factor Reprogramming Unleashes Selective Translation Promoting Castration Resistance and Immune Evasion in Lethal Prostate Cancer

Author

Santasusagna, Sandra, primary, Zhu, Shijia, additional, Jawalagatti, Vijayakumar, additional, Carceles-Cordon, Marc, additional, Ertel, Adam, additional, Garcia-Longarte, Saioa, additional, Song, Won-Min, additional, Fujiwara, Naoto, additional, Li, Peiyao, additional, Mendizabal, Isabel, additional, Petrylak, Daniel P., additional, Kelly, William Kevin, additional, Reddy, E. Premkumar, additional, Wang, Liguo, additional, Schiewer, Matthew J., additional, Lujambio, Amaia, additional, Karnes, Jeffrey, additional, Knudsen, Karen E., additional, Cordon-Cardo, Carlos, additional, Dong, Haidong, additional, Huang, Haojie, additional, Carracedo, Arkaitz, additional, Hoshida, Yujin, additional, Rodriguez-Bravo, Veronica, additional, and Domingo-Domenech, Josep, additional

Published
2023
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47. A genome-wide gain-of-function screen identifies CDKN2C as a HBV host factor

Author

Eller, Carla, Heydmann, Laura, Colpitts, Che C., El Saghire, Houssein, Piccioni, Federica, Jühling, Frank, Majzoub, Karim, Pons, Caroline, Bach, Charlotte, Lucifora, Julie, Lupberger, Joachim, Nassal, Michael, Cowley, Glenn S., Fujiwara, Naoto, Hsieh, Sen-Yung, Hoshida, Yujin, Felli, Emanuele, Pessaux, Patrick, Sureau, Camille, Schuster, Catherine, Root, David E., Verrier, Eloi R., and Baumert, Thomas F.

Published
2020
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48. Subclass mapping: identifying common subtypes in independent disease data sets.

Author

Hoshida, Yujin, Brunet, Jean-Philippe, Tamayo, Pablo, Golub, Todd R, and Mesirov, Jill P

Subjects
Humans, Breast Neoplasms, Disease, Receptors, Estrogen, Survival Analysis, Lymphoma, Large B-Cell, Diffuse, General Science & Technology
Abstract

Whole genome expression profiles are widely used to discover molecular subtypes of diseases. A remaining challenge is to identify the correspondence or commonality of subtypes found in multiple, independent data sets generated on various platforms. While model-based supervised learning is often used to make these connections, the models can be biased to the training data set and thus miss inherent, relevant substructure in the test data. Here we describe an unsupervised subclass mapping method (SubMap), which reveals common subtypes between independent data sets. The subtypes within a data set can be determined by unsupervised clustering or given by predetermined phenotypes before applying SubMap. We define a measure of correspondence for subtypes and evaluate its significance building on our previous work on gene set enrichment analysis. The strength of the SubMap method is that it does not impose the structure of one data set upon another, but rather uses a bi-directional approach to highlight the common substructures in both. We show how this method can reveal the correspondence between several cancer-related data sets. Notably, it identifies common subtypes of breast cancer associated with estrogen receptor status, and a subgroup of lymphoma patients who share similar survival patterns, thus improving the accuracy of a clinical outcome predictor.

Published
2007

49. Contributors

Author

Athuluri-Divakar, Sai Krishna, primary, Barnes, Peter J., additional, Blazes, David L., additional, Chambers, Eileen Tsai, additional, Clark, Danielle V., additional, Colón-López, Daisy D., additional, DeLeo, Frank R., additional, Doroudchi, Ali, additional, Dowell, Scott F., additional, Falsey, Ann Regina, additional, Filkins, Laura, additional, Hoshida, Yujin, additional, Hsueh, Ming-Feng, additional, Jones, Letitia D., additional, Khatri, Purvesh, additional, Kobayashi, Scott D., additional, Koehler, Jeffrey W., additional, Kraus, Virginia Byers, additional, Lambova, Sevdalina, additional, Langley, Raymond J., additional, Le Roch, Karine G., additional, Limou, Sophie, additional, Modena, Brian D., additional, Moody, M. Anthony, additional, Müller-Ladner, Ulf, additional, Patel, Keyur, additional, Patel, Parth, additional, Patsopoulos, Nikolaos A., additional, Ploumakis, Athanasios, additional, Robert, Schlaberg, additional, Sathish, Varshini, additional, Schully, Kevin L., additional, Shackel, Nicholas A, additional, Shaw, Brian I., additional, Stefan, Christopher P., additional, Surana, Neeraj K., additional, Sweeney, Timothy E., additional, Tan, Yong B., additional, Thompson, Amelia B., additional, Tsalik, Ephraim L., additional, Weiner, Howard L., additional, Wester, C. William, additional, Willard, Huntington F., additional, Williams, Desiree, additional, Winkler, Cheryl A., additional, Wong, Hector R., additional, and Woods, Christopher W., additional

Published
2019
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