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202. Integrated Stem Cell Signature and Cytomolecular Risk Determination in Pediatric Acute Myeloid Leukemia

Author

Huang, Benjamin J., primary, Smith, Jenny L., additional, Ries, Rhonda E., additional, Leonti, Amanda R., additional, Crowgey, Erin Lynn, additional, Furlan, Scott N., additional, Shaw, Timothy, additional, Wei, Lisa, additional, Wang, Yi-Cheng, additional, Gerbing, Robert B., additional, Alonzo, Todd A., additional, Cooper, Todd M., additional, Kolb, Edward A., additional, Ma, Xiaotu, additional, Farrar, Jason E., additional, Triche, Timothy Junius, additional, and Meshinchi, Soheil, additional

Published
2020
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203. Creating a Variant Database for the American Society of Hematalogy By Consensus Variant Classification of Common Genes Associated with Hematologic Malignancies

Author

Nadarajah, Niroshan, primary, Wagner, Alex, additional, Bejar, Rafael, additional, Ewalt, Mark, additional, Kim, Annette S., additional, Le Beau, Michelle M., additional, Ma, Xiaotu, additional, Meggendorfer, Manja, additional, Shammo, Jamile M., additional, Ryan, Gabriella, additional, Siddon, Alexa J., additional, Steensma, David P., additional, Walter, Matthew J., additional, Zehir, Ahmet, additional, Zhang, Jinghui, additional, and Haferlach, Torsten, additional

Published
2020
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204. Genome and Transcriptome Profiling of Monosomy 7 AML Defines Novel Risk and Therapeutic Cohorts

Author

Ries, Rhonda E., primary, Triche, Timothy Junius, additional, Smith, Jenny L., additional, Leonti, Amanda R., additional, Alonzo, Todd A., additional, Farrar, Jason E., additional, Chen, Xiaolong, additional, Liu, Yanling, additional, Shaw, Timothy, additional, Huang, Benjamin J., additional, Wang, Yi-Cheng, additional, Gerbing, Robert B., additional, Hirsch, Betsy A, additional, Raimondi, Susana C., additional, Gamis, Alan S., additional, Aplenc, Richard, additional, Zhang, Jinghui, additional, Kolb, E. Anders, additional, Ma, Xiaotu, additional, and Meshinchi, Soheil, additional

Published
2020
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205. Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations

Author

Brady, Samuel W., primary, Liu, Yanling, additional, Ma, Xiaotu, additional, Gout, Alexander M., additional, Hagiwara, Kohei, additional, Zhou, Xin, additional, Wang, Jian, additional, Macias, Michael, additional, Chen, Xiaolong, additional, Easton, John, additional, Mulder, Heather L., additional, Rusch, Michael, additional, Wang, Lu, additional, Nakitandwe, Joy, additional, Lei, Shaohua, additional, Davis, Eric M., additional, Naranjo, Arlene, additional, Cheng, Cheng, additional, Maris, John M., additional, Downing, James R., additional, Cheung, Nai-Kong V., additional, Hogarty, Michael D., additional, Dyer, Michael A., additional, and Zhang, Jinghui, additional

Published
2020
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206. St. Jude Cloud—a Pediatric Cancer Genomic Data Sharing Ecosystem

Author

McLeod, Clay, primary, Gout, Alexander M., additional, Zhou, Xin, additional, Rahbarinia, Delaram, additional, Thrasher, Andrew, additional, Newman, Scott, additional, Birch, Kirby, additional, Macias, Michael, additional, Finkelstein, David, additional, Sunny, Jobin, additional, Mudunuri, Rahul, additional, Orr, Brent A., additional, Treadway, Madison, additional, Davidson, Bob, additional, Ard, Tracy, additional, Swistak, Andrew, additional, Wiggins, Stephanie, additional, Foy, Scott, additional, Brady, Samuel W., additional, Wang, Jian, additional, Sioson, Edgar, additional, Wang, Shuoguo, additional, Michael, J. Robert, additional, Liu, Yu, additional, Ma, Xiaotu, additional, Patel, Aman, additional, Edmonson, Michael N., additional, Wilkinson, Mark R., additional, Frantz, Andrew, additional, Chang, Ti-Cheng, additional, Tian, Liqing, additional, Lei, Shaohua, additional, Meyer, Christopher, additional, Thangaraj, Naina, additional, Tater, Pamella, additional, Kandali, Vijay, additional, Ma, Singer, additional, Nguyen, Tuan, additional, Serang, Omar, additional, McGuire, Irina, additional, Robison, Nedra, additional, Gentry, Darrell, additional, Tang, Xing, additional, Palmer, Lance, additional, Wu, Gang, additional, Suh, Ed, additional, Tanner, Leigh, additional, McMurry, James, additional, Lear, Matthew, additional, Wang, Zhaoming, additional, Wilson, Carmen, additional, Cheng, Yong, additional, Weiss, Mitch, additional, Armstrong, Gregory T., additional, Robison, Leslie L., additional, Yasui, Yutaka, additional, Nichols, Kim E., additional, Ellison, David W., additional, Bangur, Chitanya, additional, Mullighan, Charles G., additional, Baker, Suzanne J., additional, Dyer, Michael, additional, Miller, Geralyn, additional, Rusch, Michael, additional, Daly, Richard, additional, Perry, Keith, additional, Downing, James R., additional, and Zhang, Jinghui, additional

Published
2020
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207. Abstract 5399: The NSD2 p.E1099K mutation is enriched at relapse and confers drug resistance in a cell context dependent manner in pediatric acute lymphoblastic leukemia

Author

Pierro, Joanna, primary, Saliba, Jason, additional, Narang, Sonali, additional, Sethia, Gunjan, additional, Fleur-Lominy, Shella Saint, additional, Chowdhury, Ashfiyah, additional, Moriyama, Takaya, additional, Schmiegelow, Kjeld, additional, Yang, Jun J., additional, Loh, Mignon L., additional, Brown, Patrick A., additional, Zhang, Jinghui, additional, Ma, Xiaotu, additional, Tsirigos, Aristotelis, additional, Evensen, Nikki A., additional, and Carroll, William L., additional

Published
2020
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208. The NSD2 p.E1099K Mutation Is Enriched at Relapse and Confers Drug Resistance in a Cell Context–Dependent Manner in Pediatric Acute Lymphoblastic Leukemia

Author

Pierro, Joanna, primary, Saliba, Jason, additional, Narang, Sonali, additional, Sethia, Gunjan, additional, Saint Fleur-Lominy, Shella, additional, Chowdhury, Ashfiyah, additional, Qualls, Anita, additional, Fay, Hannah, additional, Kilberg, Harrison L., additional, Moriyama, Takaya, additional, Fuller, Tori J., additional, Teachey, David T., additional, Schmiegelow, Kjeld, additional, Yang, Jun J., additional, Loh, Mignon L., additional, Brown, Patrick A., additional, Zhang, Jinghui, additional, Ma, Xiaotu, additional, Tsirigos, Aristotelis, additional, Evensen, Nikki A., additional, and Carroll, William L., additional

Published
2020
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209. FPGS relapse-specific mutations in relapsed childhood acute lymphoblastic leukemia

Author

Yu, Sung-Liang, primary, Zhang, Hui, additional, Ho, Bing-Ching, additional, Yu, Chih-Hsiang, additional, Chang, Chia-Ching, additional, Hsu, Yin-Chen, additional, Ni, Yu-Ling, additional, Lin, Kai-Hsin, additional, Jou, Shiann-Tarng, additional, Lu, Meng-Yao, additional, Chen, Shu-Huey, additional, Wu, Kang-Hsi, additional, Wang, Shih-Chung, additional, Chang, Hsiu-Hao, additional, Pui, Ching-Hon, additional, Yang, Jun J., additional, Zhang, Jinghui, additional, Lin, Dong-Tsamn, additional, Lin, Shu-Wha, additional, Ma, Xiaotu, additional, and Yang, Yung-Li, additional

Published
2020
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211. Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X

Author

Liu, Yu, primary, Li, Chunliang, additional, Shen, Shuhong, additional, Chen, Xiaolong, additional, Szlachta, Karol, additional, Edmonson, Michael N., additional, Shao, Ying, additional, Ma, Xiaotu, additional, Hyle, Judith, additional, Wright, Shaela, additional, Ju, Bensheng, additional, Rusch, Michael C., additional, Liu, Yanling, additional, Li, Benshang, additional, Macias, Michael, additional, Tian, Liqing, additional, Easton, John, additional, Qian, Maoxiang, additional, Yang, Jun J., additional, Hu, Shaoyan, additional, Look, A. Thomas, additional, and Zhang, Jinghui, additional

Published
2020
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212. Mutational Landscape and Patterns of Clonal Evolution in Relapsed Pediatric Acute Lymphoblastic Leukemia

Author

Waanders, Esmé, primary, Gu, Zhaohui, additional, Dobson, Stephanie M., additional, Antić, Željko, additional, Crawford, Jeremy Chase, additional, Ma, Xiaotu, additional, Edmonson, Michael N., additional, Payne-Turner, Debbie, additional, van de Vorst, Maartje, additional, Jongmans, Marjolijn C.J., additional, McGuire, Irina, additional, Zhou, Xin, additional, Wang, Jian, additional, Shi, Lei, additional, Pounds, Stanley, additional, Pei, Deqing, additional, Cheng, Cheng, additional, Song, Guangchun, additional, Fan, Yiping, additional, Shao, Ying, additional, Rusch, Michael, additional, McCastlain, Kelly, additional, Yu, Jiangyan, additional, van Boxtel, Ruben, additional, Blokzijl, Francis, additional, Iacobucci, Ilaria, additional, Roberts, Kathryn G., additional, Wen, Ji, additional, Wu, Gang, additional, Ma, Jing, additional, Easton, John, additional, Neale, Geoffrey, additional, Olsen, Scott R., additional, Nichols, Kim E., additional, Pui, Ching-Hon, additional, Zhang, Jinghui, additional, Evans, William E., additional, Relling, Mary V., additional, Yang, Jun J., additional, Thomas, Paul G., additional, Dick, John E., additional, Kuiper, Roland P., additional, and Mullighan, Charles G., additional

Published
2020
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213. Systematic Study of Al Impurity for NCM622 Cathode Materials

Author

Zhang, Ruihan, primary, Zheng, Yadong, additional, Yao, Zeyi, additional, Vanaphuti, Panawan, additional, Ma, Xiaotu, additional, Bong, Sungyool, additional, Chen, Mengyuan, additional, Liu, Yangtao, additional, Cheng, Feng, additional, Yang, Zhenzhen, additional, and Wang, Yan, additional

Published
2020
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218. Relapse-Fated Latent Diagnosis Subclones in Acute B Lineage Leukemia Are Drug Tolerant and Possess Distinct Metabolic Programs

Author

Dobson, Stephanie M., primary, García-Prat, Laura, additional, Vanner, Robert J., additional, Wintersinger, Jeffrey, additional, Waanders, Esmé, additional, Gu, Zhaohui, additional, McLeod, Jessica, additional, Gan, Olga I., additional, Grandal, Ildiko, additional, Payne-Turner, Debbie, additional, Edmonson, Michael N., additional, Ma, Xiaotu, additional, Fan, Yiping, additional, Voisin, Veronique, additional, Chan-Seng-Yue, Michelle, additional, Xie, Stephanie Z., additional, Hosseini, Mohsen, additional, Abelson, Sagi, additional, Gupta, Pankaj, additional, Rusch, Michael, additional, Shao, Ying, additional, Olsen, Scott R., additional, Neale, Geoffrey, additional, Chan, Steven M., additional, Bader, Gary, additional, Easton, John, additional, Guidos, Cynthia J., additional, Danska, Jayne S., additional, Zhang, Jinghui, additional, Minden, Mark D., additional, Morris, Quaid, additional, Mullighan, Charles G., additional, and Dick, John E., additional

Published
2020
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219. Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia

Author

Li, Benshang, primary, Brady, Samuel W., additional, Ma, Xiaotu, additional, Shen, Shuhong, additional, Zhang, Yingchi, additional, Li, Yongjin, additional, Szlachta, Karol, additional, Dong, Li, additional, Liu, Yu, additional, Yang, Fan, additional, Wang, Ningling, additional, Flasch, Diane A., additional, Myers, Matthew A., additional, Mulder, Heather L., additional, Ding, Lixia, additional, Liu, Yanling, additional, Tian, Liqing, additional, Hagiwara, Kohei, additional, Xu, Ke, additional, Zhou, Xin, additional, Sioson, Edgar, additional, Wang, Tianyi, additional, Yang, Liu, additional, Zhao, Jie, additional, Zhang, Hui, additional, Shao, Ying, additional, Sun, Hongye, additional, Sun, Lele, additional, Cai, Jiaoyang, additional, Sun, Hui-Ying, additional, Lin, Ting-Nien, additional, Du, Lijuan, additional, Li, Hui, additional, Rusch, Michael, additional, Edmonson, Michael N., additional, Easton, John, additional, Zhu, Xiaofan, additional, Zhang, Jingliao, additional, Cheng, Cheng, additional, Raphael, Benjamin J., additional, Tang, Jingyan, additional, Downing, James R., additional, Alexandrov, Ludmil B., additional, Zhou, Bin-Bing S., additional, Pui, Ching-Hon, additional, Yang, Jun J., additional, and Zhang, Jinghui, additional

Published
2020
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223. Genomic subtyping and therapeutic targeting of acute erythroleukemia.

Author

Iacobucci, Ilaria, Iacobucci, Ilaria, Wen, Ji, Meggendorfer, Manja, Choi, John K, Shi, Lei, Pounds, Stanley B, Carmichael, Catherine L, Masih, Katherine E, Morris, Sarah M, Lindsley, R Coleman, Janke, Laura J, Alexander, Thomas B, Song, Guangchun, Qu, Chunxu, Li, Yongjin, Payne-Turner, Debbie, Tomizawa, Daisuke, Kiyokawa, Nobutaka, Valentine, Marcus, Valentine, Virginia, Basso, Giuseppe, Locatelli, Franco, Enemark, Eric J, Kham, Shirley KY, Yeoh, Allen EJ, Ma, Xiaotu, Zhou, Xin, Sioson, Edgar, Rusch, Michael, Ries, Rhonda E, Stieglitz, Elliot, Hunger, Stephen P, Wei, Andrew H, To, L Bik, Lewis, Ian D, D'Andrea, Richard J, Kile, Benjamin T, Brown, Anna L, Scott, Hamish S, Hahn, Christopher N, Marlton, Paula, Pei, Deqing, Cheng, Cheng, Loh, Mignon L, Ebert, Benjamin L, Meshinchi, Soheil, Haferlach, Torsten, Mullighan, Charles G, Iacobucci, Ilaria, Iacobucci, Ilaria, Wen, Ji, Meggendorfer, Manja, Choi, John K, Shi, Lei, Pounds, Stanley B, Carmichael, Catherine L, Masih, Katherine E, Morris, Sarah M, Lindsley, R Coleman, Janke, Laura J, Alexander, Thomas B, Song, Guangchun, Qu, Chunxu, Li, Yongjin, Payne-Turner, Debbie, Tomizawa, Daisuke, Kiyokawa, Nobutaka, Valentine, Marcus, Valentine, Virginia, Basso, Giuseppe, Locatelli, Franco, Enemark, Eric J, Kham, Shirley KY, Yeoh, Allen EJ, Ma, Xiaotu, Zhou, Xin, Sioson, Edgar, Rusch, Michael, Ries, Rhonda E, Stieglitz, Elliot, Hunger, Stephen P, Wei, Andrew H, To, L Bik, Lewis, Ian D, D'Andrea, Richard J, Kile, Benjamin T, Brown, Anna L, Scott, Hamish S, Hahn, Christopher N, Marlton, Paula, Pei, Deqing, Cheng, Cheng, Loh, Mignon L, Ebert, Benjamin L, Meshinchi, Soheil, Haferlach, Torsten, and Mullighan, Charles G

Abstract

Acute erythroid leukemia (AEL) is a high-risk leukemia of poorly understood genetic basis, with controversy regarding diagnosis in the spectrum of myelodysplasia and myeloid leukemia. We compared genomic features of 159 childhood and adult AEL cases with non-AEL myeloid disorders and defined five age-related subgroups with distinct transcriptional profiles: adult, TP53 mutated; NPM1 mutated; KMT2A mutated/rearranged; adult, DDX41 mutated; and pediatric, NUP98 rearranged. Genomic features influenced outcome, with NPM1 mutations and HOXB9 overexpression being associated with a favorable prognosis and TP53, FLT3 or RB1 alterations associated with poor survival. Targetable signaling mutations were present in 45% of cases and included recurrent mutations of ALK and NTRK1, the latter of which drives erythroid leukemogenesis sensitive to TRK inhibition. This genomic landscape of AEL provides the framework for accurate diagnosis and risk stratification of this disease, and the rationale for testing targeted therapies in this high-risk leukemia.

Published
2019

224. A systematic analysis of genetic interactions and their underlying biology in childhood cancer.

Author

Daub, Josephine T., Amini, Saman, Kersjes, Denise J. E., Ma, Xiaotu, Jäger, Natalie, Zhang, Jinghui, Pfister, Stefan M., Holstege, Frank C. P., and Kemmeren, Patrick

Subjects
CHILDHOOD cancer, CARCINOGENESIS, BIOLOGY, DEVELOPED countries, GENE mapping
Abstract

Childhood cancer is a major cause of child death in developed countries. Genetic interactions between mutated genes play an important role in cancer development. They can be detected by searching for pairs of mutated genes that co-occur more (or less) often than expected. Co-occurrence suggests a cooperative role in cancer development, while mutual exclusivity points to synthetic lethality, a phenomenon of interest in cancer treatment research. Little is known about genetic interactions in childhood cancer. We apply a statistical pipeline to detect genetic interactions in a combined dataset comprising over 2,500 tumors from 23 cancer types. The resulting genetic interaction map of childhood cancers comprises 15 co-occurring and 27 mutually exclusive candidates. The biological explanation of most candidates points to either tumor subtype, pathway epistasis or cooperation while synthetic lethality plays a much smaller role. Thus, other explanations beyond synthetic lethality should be considered when interpreting genetic interaction test results. Josephine Daub, Saman Amini, et al. developed a genetic interaction map of childhood cancers by analyzing over 2,500 tumors from 23 types of childhood cancer. Their results provide a valuable resource for investigating the biological underpinnings of pediatric cancer. [ABSTRACT FROM AUTHOR]

Published
2021
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226. The Genomic Landscape of Childhood Acute Lymphoblastic Leukemia

Author

Roberts, Kathryn G., primary, Brady, Samuel W., primary, Gu, Zhaohui, primary, Shi, Lei, primary, Pounds, Stanley, primary, Pei, Deqing, primary, Cheng, Cheng, primary, Dai, Yunfeng, primary, Devidas, Meenakshi, primary, Qu, Chunxu, primary, Hill, Ashley, primary, Ma, Xiaotu, primary, Wei, Lei, primary, Arunachalam, Sasi, primary, Hagiwara, Kohei, primary, Liu, Yangling, primary, Flasch, Diane, primary, Liu, Yu, primary, Parker, Matthew, primary, Chen, Xiaolong, primary, Li, Yongjin, primary, Fan, Yiping, primary, Michael, Robert, primary, Rusch, Michael, primary, Wilkinson, Mark, primary, Foy, Scott, primary, Hedges, Dale, primary, Newman, Scott, primary, Zhou, Xin, primary, Wang, Jian, primary, Reshmi, Shalini C., primary, Gastier-Foster, Julie M., primary, Gesuwan, Patee, primary, Smith, Malcolm A, primary, Gerhard, Daniela S., primary, Winick, Naomi, primary, Carroll, Andrew J., primary, Heerema, Nyla A., primary, Harvey, Richard C., primary, Willman, Cheryl L., primary, Larsen, Eric, primary, Raetz, Elizabeth A., primary, Borowitz, Michael J., primary, Wood, Brent L, primary, Carroll, William L., primary, Zweidler-McKay, Patrick A., primary, Rabin, Karen R., primary, Mattano, Leonard A., primary, Maloney, Kelly, primary, Winter, Stuart S., primary, Burke, Michael J., primary, Salzer, Wanda L., primary, Dunsmore, Kimberly P., primary, Angiolillo, Anne, primary, Crews, Kristine R, primary, Downing, James R., primary, Jeha, Sima, primary, Evans, William E., primary, Pui, Ching-Hon, primary, Yang, Jun J., primary, Relling, Mary V., primary, Hunger, Stephen P., primary, Loh, Mignon L., primary, Zhang, Jinghui, primary, and Mullighan, Charles G., primary

Published
2019
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227. Comprehensive Genomic Profiling of Pediatric Therapy-Related Myeloid Neoplasms Identifies Mecom Dysregulation to be Associated with Poor Outcome

Author

Schwartz, Jason R, primary, Ma, Jing, additional, Walsh, Michael P, additional, Chen, Xiaolong, additional, Lamprecht, Tamara, additional, Kamens, Jennifer, additional, Newman, Scott, additional, Zhang, Jinghui, additional, Gruber, Tanja A., additional, Ma, Xiaotu, additional, and Klco, Jeffery M., additional

Published
2019
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230. Host–Guest Polypyrrole Nanocomplex for Three‐Stimuli‐Responsive Drug Delivery and Imaging‐Guided Chemo‐Photothermal Synergetic Therapy of Refractory Thyroid Cancer

Author

Ma, Xiaotu, primary, Li, Xiaoda, additional, Shi, Jiyun, additional, Yao, Meinan, additional, Zhang, Xu, additional, Hou, Rui, additional, Shao, Nan, additional, Luo, Qi, additional, Gao, Yu, additional, Du, Shuaifan, additional, Liang, Xiaolong, additional, and Wang, Fan, additional

Published
2019
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231. Abstract 2872: Acquisition of drug resistance mutations during chemotherapy treatment in pediatric acute lymphoblastic leukemia

Author

Li, Benshang, primary, Brady, Samuel W., additional, Ma, Xiaotu, additional, Shen, Shuhong, additional, Zhang, Yingchi, additional, Li, Yongjin, additional, Liu, Yu, additional, Wang, Ningling, additional, Flasch, Diane, additional, Myers, Matthew, additional, Mulder, Heather, additional, Ding, Lixia, additional, Lu, Yanling, additional, Tian, Liqing, additional, Hagiwara, Kohei, additional, Xu, Ke, additional, Sioson, Edgar, additional, Wang, Tianyi, additional, Yang, Liu, additional, Zhao, Jie, additional, Zhang, Hui, additional, Shao, Ying, additional, Sun, Hongye, additional, Sun, Lele, additional, Cai, Jiaoyang, additional, Lin, Ting-Nien, additional, Du, Lijuan, additional, Yang, Fan, additional, Rusch, Michael, additional, Edmonson, Michael, additional, Easton, John, additional, Zhu, Xiaofan, additional, Zhang, Jingliao, additional, Cheng, Cheng, additional, Raphael, Benjamin, additional, Tang, Jingyan, additional, Downing, James, additional, Zhou, Bin-Bing, additional, Pui, Ching-Hon, additional, Yang, Jun, additional, and Zhang, Jinghui, additional

Published
2019
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233. The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment

Author

Brady, Samuel W., primary, Ma, Xiaotu, additional, Bahrami, Armita, additional, Satas, Gryte, additional, Wu, Gang, additional, Newman, Scott, additional, Rusch, Michael, additional, Putnam, Daniel K., additional, Mulder, Heather L., additional, Yergeau, Donald A., additional, Edmonson, Michael N., additional, Easton, John, additional, Alexandrov, Ludmil B., additional, Chen, Xiang, additional, Mardis, Elaine R., additional, Wilson, Richard K., additional, Downing, James R., additional, Pappo, Alberto S., additional, Raphael, Benjamin J., additional, Dyer, Michael A., additional, and Zhang, Jinghui, additional

Published
2019
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234. Genomic subtyping and therapeutic targeting of acute erythroleukemia

Author

Iacobucci, Ilaria, primary, Wen, Ji, additional, Meggendorfer, Manja, additional, Choi, John K., additional, Shi, Lei, additional, Pounds, Stanley B., additional, Carmichael, Catherine L., additional, Masih, Katherine E., additional, Morris, Sarah M., additional, Lindsley, R. Coleman, additional, Janke, Laura J., additional, Alexander, Thomas B., additional, Song, Guangchun, additional, Qu, Chunxu, additional, Li, Yongjin, additional, Payne-Turner, Debbie, additional, Tomizawa, Daisuke, additional, Kiyokawa, Nobutaka, additional, Valentine, Marcus, additional, Valentine, Virginia, additional, Basso, Giuseppe, additional, Locatelli, Franco, additional, Enemark, Eric J., additional, Kham, Shirley K. Y., additional, Yeoh, Allen E. J., additional, Ma, Xiaotu, additional, Zhou, Xin, additional, Sioson, Edgar, additional, Rusch, Michael, additional, Ries, Rhonda E., additional, Stieglitz, Elliot, additional, Hunger, Stephen P., additional, Wei, Andrew H., additional, To, L Bik, additional, Lewis, Ian D., additional, D’Andrea, Richard J., additional, Kile, Benjamin T., additional, Brown, Anna L., additional, Scott, Hamish S., additional, Hahn, Christopher N., additional, Marlton, Paula, additional, Pei, Deqing, additional, Cheng, Cheng, additional, Loh, Mignon L., additional, Ebert, Benjamin L., additional, Meshinchi, Soheil, additional, Haferlach, Torsten, additional, and Mullighan, Charles G., additional

Published
2019
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235. Publisher Correction: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions

Author

Bolouri, Hamid, primary, Farrar, Jason E, additional, Triche, Timothy, additional, Ries, Rhonda E, additional, Lim, Emilia L, additional, Alonzo, Todd A, additional, Ma, Yussanne, additional, Moore, Richard, additional, Mungall, Andrew J, additional, Marra, Marco A, additional, Zhang, Jinghui, additional, Ma, Xiaotu, additional, Liu, Yu, additional, Liu, Yanling, additional, Auvil, Jaime M Guidry, additional, Davidsen, Tanja M, additional, Gesuwan, Patee, additional, Hermida, Leandro C, additional, Salhia, Bodour, additional, Capone, Stephen, additional, Ramsingh, Giridharan, additional, Zwaan, Christian Michel, additional, Noort, Sanne, additional, Piccolo, Stephen R, additional, Kolb, E Anders, additional, Gamis, Alan S, additional, Smith, Malcolm A, additional, Gerhard, Daniela S, additional, and Meshinchi, Soheil, additional

Published
2019
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237. Lectin-Mediated pH-Sensitive Doxorubicin Prodrug for Pre-Targeted Chemotherapy of Colorectal Cancer with Enhanced Efficacy and Reduced Side Effects

Author

Yao, Meinan, primary, Ma, Xiaotu, additional, Zhang, Xin, additional, Shi, Linqing, additional, Liu, Tianyu, additional, Liang, Xiaolong, additional, Zhao, Huiyun, additional, Li, Xiaoda, additional, Li, Liqiang, additional, Gao, Hannan, additional, Jia, Bing, additional, and Wang, Fan, additional

Published
2019
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238. Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to Telo-box motif enrichment

Author

Zhu Xin-Guang, Wang Zhuo, Liu Lei, Wang Yu, Wang Jie, and Ma Xiaotu

Subjects
Evolution, QH359-425
Abstract

Abstract Background Chloroplasts and mitochondria evolved from the endosymbionts of once free-living eubacteria, and they transferred most of their genes to the host nuclear genome during evolution. The mechanisms used by plants to coordinate the expression of such transferred genes, as well as other genes in the host nuclear genome, are still poorly understood. Results In this paper, we use nuclear-encoded chloroplast (cpRPGs), as well as mitochondrial (mtRPGs) and cytoplasmic (euRPGs) ribosomal protein genes to study the coordination of gene expression between organelles and the host. Results show that the mtRPGs, but not the cpRPGs, exhibit strongly synchronized expression with euRPGs in all investigated land plants and that this phenomenon is linked to the presence of a telo-box DNA motif in the promoter regions of mtRPGs and euRPGs. This motif is also enriched in the promoter regions of genes involved in DNA replication. Sequence analysis further indicates that mtRPGs, in contrast to cpRPGs, acquired telo-box from the host nuclear genome. Conclusions Based on our results, we propose a model of plant nuclear genome evolution where coordination of activities in mitochondria and chloroplast and other cellular functions, including cell cycle, might have served as a strong selection pressure for the differential acquisition of telo-box between mtRPGs and cpRPGs. This research also highlights the significance of physiological needs in shaping transcriptional regulatory evolution.

Published
2011
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239. The genomic landscape of pediatric acute lymphoblastic leukemia

Author

Brady, Samuel W., Roberts, Kathryn G., Gu, Zhaohui, Shi, Lei, Pounds, Stanley, Pei, Deqing, Cheng, Cheng, Dai, Yunfeng, Devidas, Meenakshi, Qu, Chunxu, Hill, Ashley N., Payne-Turner, Debbie, Ma, Xiaotu, Iacobucci, Ilaria, Baviskar, Pradyuamna, Wei, Lei, Arunachalam, Sasi, Hagiwara, Kohei, Liu, Yanling, Flasch, Diane A., Liu, Yu, Parker, Matthew, Chen, Xiaolong, Elsayed, Abdelrahman H., Pathak, Omkar, Li, Yongjin, Fan, Yiping, Michael, J. Robert, Rusch, Michael, Wilkinson, Mark R., Foy, Scott, Hedges, Dale J., Newman, Scott, Zhou, Xin, Wang, Jian, Reilly, Colleen, Sioson, Edgar, Rice, Stephen V., Pastor Loyola, Victor, Wu, Gang, Rampersaud, Evadnie, Reshmi, Shalini C., Gastier-Foster, Julie, Guidry Auvil, Jaime M., Gesuwan, Patee, Smith, Malcolm A., Winick, Naomi, Carroll, Andrew J., Heerema, Nyla A., Harvey, Richard C., Willman, Cheryl L., Larsen, Eric, Raetz, Elizabeth A., Borowitz, Michael J., Wood, Brent L., Carroll, William L., Zweidler-McKay, Patrick A., Rabin, Karen R., Mattano, Leonard A., Maloney, Kelly W., Winter, Stuart S., Burke, Michael J., Salzer, Wanda, Dunsmore, Kimberly P., Angiolillo, Anne L., Crews, Kristine R., Downing, James R., Jeha, Sima, Pui, Ching-Hon, Evans, William E., Yang, Jun J., Relling, Mary V., Gerhard, Daniela S., Loh, Mignon L., Hunger, Stephen P., Zhang, Jinghui, and Mullighan, Charles G.

Abstract

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Here, using whole-genome, exome and transcriptome sequencing of 2,754 childhood patients with ALL, we find that, despite a generally low mutation burden, ALL cases harbor a median of four putative somatic driver alterations per sample, with 376 putative driver genes identified varying in prevalence across ALL subtypes. Most samples harbor at least one rare gene alteration, including 70 putative cancer driver genes associated with ubiquitination, SUMOylation, noncoding transcripts and other functions. In hyperdiploid B-ALL, chromosomal gains are acquired early and synchronously before ultraviolet-induced mutation. By contrast, ultraviolet-induced mutations precede chromosomal gains in B-ALL cases with intrachromosomal amplification of chromosome 21. We also demonstrate the prognostic significance of genetic alterations within subtypes. Intriguingly, DUX4- and KMT2A-rearranged subtypes separate into CEBPA/FLT3- or NFATC4-expressing subgroups with potential clinical implications. Together, these results deepen understanding of the ALL genomic landscape and associated outcomes.

Published
2022
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240. CBFB-MYH11 fusion transcripts distinguish acute myeloid leukemias with distinct molecular landscapes and outcomes

Author

Huang, Benjamin J., Smith, Jenny L., Wang, Yi-Cheng, Taghizadeh, Kassra, Leonti, Amanda R., Ries, Rhonda E., Liu, Yanling, Kolekar, Pandurang, Tarlock, Katherine, Gerbing, Robert, Crowgey, Erin, Furlan, Scott N., Shaw, Timothy I., Hagiwara, Kohei, Wei, Lisa, Cooper, Todd M., Gamis, Alan S., Aplenc, Richard, Kolb, E. Anders, Farrar, Jason E., Triche, Timothy, Alonzo, Todd A., Ma, Xiaotu, and Meshinchi, Soheil

Published
2021
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241. Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL).

Author

Shaw, Timothy I., Dong, Li, Tian, Liqing, Qian, Chenxi, Liu, Yu, Ju, Bensheng, High, Anthony, Kavdia, Kanisha, Pagala, Vishwajeeth R., Shaner, Bridget, Pei, Deqing, Easton, John, Janke, Laura J., Porter, Shaina N., Ma, Xiaotu, Cheng, Cheng, Pruett-Miller, Shondra M., Choi, John, Yu, Jiyang, and Peng, Junmin

Subjects
GENETIC mutation, ONCOGENES, LYMPHOBLASTIC leukemia in children, T cells, CRISPRS
Abstract

USP7, which encodes a deubiquitylating enzyme, is among the most frequently mutated genes in pediatric T-ALL, with somatic heterozygous loss-of-function mutations (haploinsufficiency) predominantly affecting the subgroup that has aberrant TAL1 oncogene activation. Network analysis of > 200 T-ALL transcriptomes linked USP7 haploinsufficiency with decreased activities of E-proteins. E-proteins are also negatively regulated by TAL1, leading to concerted down-regulation of E-protein target genes involved in T-cell development. In T-ALL cell lines, we showed the physical interaction of USP7 with E-proteins and TAL1 by mass spectrometry and ChIP-seq. Haploinsufficient but not complete CRISPR knock-out of USP7 showed accelerated cell growth and validated transcriptional down-regulation of E-protein targets. Our study unveiled the synergistic effect of USP7 haploinsufficiency with aberrant TAL1 activation on T-ALL, implicating USP7 as a haploinsufficient tumor suppressor in T-ALL. Our findings caution against a universal oncogene designation for USP7 while emphasizing the dosage-dependent consequences of USP7 inhibitors currently under development as potential cancer therapeutics. [ABSTRACT FROM AUTHOR]

Published
2021
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242. Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia.

Author

Ma, Xiaotu, Ma, Xiaotu, Edmonson, Michael, Yergeau, Donald, Muzny, Donna M, Hampton, Oliver A, Rusch, Michael, Song, Guangchun, Easton, John, Harvey, Richard C, Wheeler, David A, Ma, Jing, Doddapaneni, HarshaVardhan, Vadodaria, Bhavin, Wu, Gang, Nagahawatte, Panduka, Carroll, William L, Chen, I-Ming, Gastier-Foster, Julie M, Relling, Mary V, Smith, Malcolm A, Devidas, Meenakshi, Guidry Auvil, Jaime M, Downing, James R, Loh, Mignon L, Willman, Cheryl L, Gerhard, Daniela S, Mullighan, Charles G, Hunger, Stephen P, Zhang, Jinghui, Ma, Xiaotu, Ma, Xiaotu, Edmonson, Michael, Yergeau, Donald, Muzny, Donna M, Hampton, Oliver A, Rusch, Michael, Song, Guangchun, Easton, John, Harvey, Richard C, Wheeler, David A, Ma, Jing, Doddapaneni, HarshaVardhan, Vadodaria, Bhavin, Wu, Gang, Nagahawatte, Panduka, Carroll, William L, Chen, I-Ming, Gastier-Foster, Julie M, Relling, Mary V, Smith, Malcolm A, Devidas, Meenakshi, Guidry Auvil, Jaime M, Downing, James R, Loh, Mignon L, Willman, Cheryl L, Gerhard, Daniela S, Mullighan, Charles G, Hunger, Stephen P, and Zhang, Jinghui

Abstract

There is incomplete understanding of genetic heterogeneity and clonal evolution during cancer progression. Here we use deep whole-exome sequencing to describe the clonal architecture and evolution of 20 pediatric B-acute lymphoblastic leukaemias from diagnosis to relapse. We show that clonal diversity is comparable at diagnosis and relapse and clonal survival from diagnosis to relapse is not associated with mutation burden. Six pathways were frequently mutated, with NT5C2, CREBBP, WHSC1, TP53, USH2A, NRAS and IKZF1 mutations enriched at relapse. Half of the leukaemias had multiple subclonal mutations in a pathway or gene at diagnosis, but mostly with only one, usually minor clone, surviving therapy to acquire additional mutations and become the relapse founder clone. Relapse-specific mutations in NT5C2 were found in nine cases, with mutations in four cases being in descendants of the relapse founder clone. These results provide important insights into the genetic basis of treatment failure in ALL and have implications for the early detection of mutations driving relapse.

Published
2015

243. Recycled cathode materials enabled superior performance for lithium-ion batteries

Author

Ma, Xiaotu, Chen, Mengyuan, Zheng, Zhangfeng, Bullen, Dennis, Wang, Jun, Harrison, Chloe, Gratz, Eric, Lin, Yulin, Yang, Zhenzhen, Zhang, Youtian, Wang, Fan, Robertson, David, Son, Seoung-Bum, Bloom, Ira, Wen, Jianguo, Ge, Mingyuan, Xiao, Xianghui, Lee, Wah-Keat, Tang, Ming, Wang, Qiang, Fu, Jinzhao, Zhang, Yubin, Sousa, Bryer C., Arsenault, Renata, Karlson, Peter, Simon, Nakia, and Wang, Yan

Abstract

Recycling spent lithium-ion batteries plays a significant role in alleviating the shortage of raw materials and environmental problems. However, recycled materials are deemed inferior to commercial materials, preventing the industry from adopting recycled materials in new batteries. Here, we demonstrate that the recycled LiNi1/3Mn1/3Co1/3O2has a superior rate and cycle performance, verified by various industry-level tests. Specifically, 1 Ah cells with the recycled LiNi1/3Mn1/3Co1/3O2have the best cycle life result reported for recycled materials and enable 4,200 cycles and 11,600 cycles at 80% and 70% capacity retention, which is 33% and 53% better than the state-of-the-art, commercial LiNi1/3Mn1/3Co1/3O2. Meanwhile, its rate performance is 88.6% better than commercial powders at 5C. From experimental and modeling results, the unique microstructure of recycled materials enables superior electrochemical performance. The recycled material outperforms commercially available equivalent, providing a green and sustainable solution for spent lithium-ion batteries.

Published
2021
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245. Erratum: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions

Author

Bolouri, Hamid, Farrar, Jason E, Triche, Timothy, Jr, Ries, Rhonda E, Lim, Emilia L, Alonzo, Todd A, Ma, Yussanne, Moore, Richard, Mungall, Andrew J, Marra, Marco A, Zhang, Jinghui, Ma, Xiaotu, Liu, Yu, Liu, Yanling, Auvil, Jaime M Guidry, Davidsen, Tanja M, Gesuwan, Patee, Hermida, Leandro C, Salhia, Bodour, Capone, Stephen, Ramsingh, Giridharan, Zwaan, Christian Michel, Noort, Sanne, Piccolo, Stephen R, Kolb, E Anders, Gamis, Alan S, Smith, Malcolm A, Gerhard, Daniela S, and Meshinchi, Soheil

Subjects
Biological sciences, Health
Abstract

Author(s): Hamid Bolouri; Jason E Farrar; Timothy Triche, Jr; Rhonda E Ries; Emilia L Lim; Todd A Alonzo; Yussanne Ma; Richard Moore; Andrew J Mungall; Marco A Marra; Jinghui Zhang; [...]

Published
2018
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246. Host–Guest Polypyrrole Nanocomplex for Three‐Stimuli‐Responsive Drug Delivery and Imaging‐Guided Chemo‐Photothermal Synergetic Therapy of Refractory Thyroid Cancer

Author

Xiaoda Li, Xiaolong Liang, Hou Rui, Fan Wang, Yu Gao, Meinan Yao, Jiyun Shi, Shao Nan, Qi Luo, Shuaifan Du, Xu Zhang, and Ma Xiaotu

Subjects
Polymers, Swine, THP-1 Cells, medicine.medical_treatment, Pharmaceutical Science, 02 engineering and technology, Polypyrrole, 01 natural sciences, Mice, chemistry.chemical_compound, Drug Delivery Systems, Tissue Distribution, Thyroid cancer, Fishes, Temperature, 021001 nanoscience & nanotechnology, Endocytosis, Tumor Burden, Drug delivery, 0210 nano-technology, Diagnostic Imaging, Cell Survival, Biomedical Engineering, Mice, Nude, 010402 general chemistry, Photoacoustic Techniques, Biomaterials, Refractory, In vivo, Human Umbilical Vein Endothelial Cells, medicine, Animals, Humans, Pyrroles, Thyroid Neoplasms, Particle Size, Chemotherapy, business.industry, Hyperthermia, Induced, Phototherapy, Photothermal therapy, medicine.disease, 0104 chemical sciences, Drug Liberation, chemistry, Doxorubicin, Hydrodynamics, Cancer research, Nanoparticles, business
Abstract

Despite the good prognosis of the low-risk thyroid cancer, there are no truly effective treatments for radioactive iodine-refractory thyroid cancer. Herein, a novel theranostic nanoplatform, as well as a smart doxorubucin (DOX) delivery system is fabricated. Gelatin-stabilized polypyrrole nanoparticles are reported for the first time. The combination of gelatin-stabilized polypyrrole and cyclodextrin-DOX complexes enabling three-stimuli-controlled drug delivery, including the enzyme-sensitive, pH-sensitive and photothermal-sensitive drug release, exhibiting a new way to equip photothermal agents with precisely controlled drug delivery. Anti-galectin-3 antibodies are utilized as the targeting molecules of nanoparticles in the first time, which surprisingly increase intracellular DOX uptake by enhanced clathrin-mediated endocytosis, showing galectin-3 can be employed as a highly efficient target of drug delivery systems. The nanoparticles achieve excellent photoacoustic imaging effect, enabled chemo-photothermal combined therapy with pinpointed drug delivery. Compared to free DOX, these multifunctional nanoparticles decrease the heart damage, but greatly increase the tumor/heart ratio of DOX concentration by 12.9-fold. The tumors are completely eradicated without any recurrence after the in vivo combined therapy. To the best of the authors' knowledge, this is also the first report to apply photoacoustic imaging-guided chemo-photothermal therapy for thyroid cancer, showing great potential to solve the dilemma in thyroid cancer therapy.

Published
2019

249. Mutational Landscape and Temporal Evolution during Treatment of Relapsed Acute Lymphoblastic Leukemia

Author

Li, Benshang, primary, Li, Yongjin, additional, Shen, Shuhong, additional, Zhang, Yingchi, additional, Brady, Samuel, additional, Ma, Xiaotu, additional, Liu, Yu, additional, Wang, Ningling, additional, Flasch, Diane, additional, Myers, Matthew, additional, Mulder, Heather, additional, Liu, Yanling, additional, Tian, Liqing, additional, Hagiwara, Kohei, additional, Zhang, Hui, additional, Shao, Ying, additional, Sun, Hongye, additional, Sun, Lele, additional, Lin, Ting-Nien, additional, Du, Lijuan, additional, Yang, Fan, additional, Rusch, Michael, additional, Edmonson, Michael, additional, Easton, John, additional, Zhu, Xiaofan, additional, Zhang, Jingliao, additional, Cheng, Cheng, additional, Raphael, Benjamin, additional, Tang, Jing-Yan, additional, Downing, James R., additional, Zhou, Bin-Bing, additional, Pui, Ching-Hon, additional, Yang, Jun J., additional, and Zhang, Jinghui, additional

Published
2018
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250. Relapse-Initiating Clones Preexisting at Diagnosis in B- Cell Acute Lymphoblastic Leukemia Help Predict Molecular Pathways of Relapse

Author

Garcia Prat, Laura, primary, Dobson, Stephanie M., additional, Chan-Seng-Yue, Michelle, additional, Vanner, Robert, additional, Murison, Alex, additional, Wintersinger, Jeffery, additional, Waanders, Esme, additional, Gan, Olga I., additional, McLeod, Jessica, additional, Payne-Turner, Debbie, additional, Edmonson, Michael, additional, Gu, Zhaohui, additional, Ma, Xiaotu, additional, Fan, Yiping, additional, Gupta, Pankaj, additional, Rusch, Michael, additional, Shao, Ying, additional, Easton, John, additional, Zhang, Jinghui, additional, Minden, Mark D., additional, Morris, Quaid, additional, Lupien, Mathieu, additional, Mullighan, Charles G., additional, and Dick, John E., additional

Published
2018
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