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11. Identification of candidate chromosome region of Sbwm1 for Soil-borne wheat mosaic virus resistance in wheat.

Author

Liu, Shubing, Bai, Guihua, Lin, Meng, Luo, Mingcheng, Zhang, Dadong, Jin, Feng, Tian, Bin, Trick, Harold, and Yan, Liuling

Subjects
Chromosome Mapping, Chromosomes, Plant, Disease Resistance, Genetic Markers, Genome, Plant, Phenotype, Plant Diseases, Plant Proteins, Plant Viruses, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Triticum
Abstract

Soil-borne wheat mosaic virus (SBWMV) causes a serious viral disease that can significantly reduce grain yield in winter wheat worldwide. Using resistant cultivars is the only feasible strategy to reduce the losses caused by SBWMV. To fine map the resistance gene Sbwm1, 205 wheat accessions was genotyped using wheat Infinium iSelect Beadchips with 90 K SNPs. Association analysis identified 35 SNPs in 12 wheat genes and one intergenic SNP in the Sbwm1 region that showed a significant association with SBWMV resistance. Those SNPs were converted into Kompetitive Allele-Specific Polymerase assays (KASP) and analyzed in two F6-derived recombinant inbred line (RIL) populations derived from the crosses between two resistant cultivars Wesley and Deliver and a susceptible line OK03825-5403-6. Linkage analysis mapped this gene on chromosome 5D at intervals of 5.1 cM and 3.4 cM in the two populations, respectively. The two flanking markers in both populations delimited the gene to a 620 kb region where 19 genes were annotated. Comparative analysis identified a syntenic region of 660 kb in Ae. tauschii with 18 annotated genes and a syntenic region in chromosome 1 of B. distachyon. The candidate region includes several disease resistance related genes and we identified a PTI1-like tyrosine-protein kinase 1 gene as a putative candidate gene for Sbwm1. The two flanking SNPs for Sbwm1 can effectively separate the resistant and susceptible lines in a new diversity panel of 159 wheat germplasm. The results from this study lay a solid foundation for the cloning, functional characterization and marker-assisted selection of Sbwm1.

Published
2020

13. Characterization of a castrate-resistant prostate cancer xenograft derived from a patient of West African ancestry

Author

Patierno, Brendon M., Foo, Wen-Chi, Allen, Tyler, Somarelli, Jason A., Ware, Kathryn E., Gupta, Santosh, Wise, Sandra, Wise, Sr., John P., Qin, Xiaodi, Zhang, Dadong, Xu, Lingfan, Li, Yanjing, Chen, Xufeng, Inman, Brant A., McCall, Shannon J., Huang, Jiaoti, Kittles, Rick A., Owzar, Kouros, Gregory, Simon, Armstrong, Andrew J., George, Daniel J., Patierno, Steven R., Hsu, David S., and Freedman, Jennifer A.

Published
2022
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14. Novel protein kinase inhibitor TT-00420 inhibits gallbladder cancer by inhibiting JNK/JUN-mediated signaling pathway

Author

Miao, Huijie, Geng, Yajun, Li, Yang, Tang, Shijie, Feng, Feiling, Li, Weijian, Li, Yongsheng, Liu, Liguo, Zhang, Rui, Qiu, Shimei, Wu, Ying, Wang, Zeyu, Wang, Ziyi, Shao, Ziyu, Liu, Ke, Zou, Lu, Yang, Mao, Zhao, Yuhao, Chen, Chen, Li, Zhizhen, Zhang, Dadong, Peng, Peng, Qiang, Xiaoyan, Wu, Frank, He, Yongning, Chen, Luonan, Xiang, Dongxi, Jiang, Xiaoqing, Li, Maolan, Liu, Yun, and Liu, Yingbin

Published
2022
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16. Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts

Author

Strand, Siri H., Rivero-Gutiérrez, Belén, Houlahan, Kathleen E., Seoane, Jose A., King, Lorraine M., Risom, Tyler, Simpson, Lunden A., Vennam, Sujay, Khan, Aziz, Cisneros, Luis, Hardman, Timothy, Harmon, Bryan, Couch, Fergus, Gallagher, Kristalyn, Kilgore, Mark, Wei, Shi, DeMichele, Angela, King, Tari, McAuliffe, Priscilla F., Nangia, Julie, Lee, Joanna, Tseng, Jennifer, Storniolo, Anna Maria, Thompson, Alastair M., Gupta, Gaorav P., Burns, Robyn, Veis, Deborah J., DeSchryver, Katherine, Zhu, Chunfang, Matusiak, Magdalena, Wang, Jason, Zhu, Shirley X., Tappenden, Jen, Ding, Daisy Yi, Zhang, Dadong, Luo, Jingqin, Jiang, Shu, Varma, Sushama, Anderson, Lauren, Straub, Cody, Srivastava, Sucheta, Curtis, Christina, Tibshirani, Rob, Angelo, Robert Michael, Hall, Allison, Owzar, Kouros, Polyak, Kornelia, Maley, Carlo, Marks, Jeffrey R., Colditz, Graham A., Hwang, E. Shelley, and West, Robert B.

Published
2022
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17. SET alpha and SET beta mRNA isoforms in chronic lymphocytic leukaemia

Author

Brander, Danielle M, Friedman, Daphne R, Volkheimer, Alicia D, Christensen, Dale J, Rassenti, Laura Z, Kipps, Thomas J, Guadalupe, Eross, Chen, Youwei, Zhang, Dadong, Wang, Xi, Davis, Carter, Owzar, Kouros, and Weinberg, J Brice

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Lymphoma, Cancer, Rare Diseases, Clinical Research, Hematology, Genetics, 2.1 Biological and endogenous factors, Aetiology, Adult, Aged, Aged, 80 and over, Alternative Splicing, DNA-Binding Proteins, Disease-Free Survival, Female, Histone Chaperones, Humans, Leukemia, Lymphocytic, Chronic, B-Cell, Male, Middle Aged, Neoplasm Proteins, Protein Isoforms, RNA, Messenger, RNA, Neoplasm, Survival Rate, Transcription Factors, chronic lymphocytic leukaemia, SET, PP2A, alternative RNA splicing, phosphatase, SET, Cardiorespiratory Medicine and Haematology, Immunology, Cardiovascular medicine and haematology
Abstract

Alteration in RNA splicing is implicated in carcinogenesis and progression. Mutations in spliceosome genes and alternative splicing of other genes have been noted in chronic lymphocytic leukaemia (CLL), a common B cell malignancy with heterogeneous outcomes. We previously demonstrated that differences in the amount of SET oncoprotein (a physiological inhibitor of the serine/threonine phosphatase, PP2A) is associated with clinical aggressiveness in patients with CLL. It is unknown if alternative splicing of gene transcripts regulating kinases and phosphatases affects disease pathobiology and CLL progression. We show here for the first time that mRNA levels of the alternatively spliced SET isoforms, SETA and SETB (SETα and SETβ), significantly correlate with disease severity (overall survival and time-to-first-treatment) in CLL patients. In addition, we demonstrate that relative increase of SETA to SETB mRNA can discriminate patients with a more aggressive disease course within the otherwise favourable CLL risk classifications of IGHV mutated and favourable hierarchical fluorescence in situ hybridisation groups. We validate our finding by showing comparable relationships of SET mRNA with disease outcomes using samples from an independent CLL cohort from a separate institution. These findings indicate that alternative splicing of SET, and potentially other signalling cascade molecules, influences CLL biology and patient outcomes.

Published
2019

25. Association of breast milk gamma-linolenic acid with infant anthropometric outcomes in urban, low-income Bangladeshi families: a prospective, birth cohort study

Author

Mychaleckyj, Josyf C., Zhang, Dadong, Nayak, Uma, Ross Colgate, E., Carmolli, Marya, Dickson, Dorothy, and Ahmed, Tahmeed

Subjects
Essential fatty acids -- Health aspects, Family -- Health aspects, Infants -- Health aspects, Child development -- Health aspects, Fatty acids -- Health aspects, Zinc in the body -- Health aspects, Urban poor -- Health aspects, Food/cooking/nutrition, Health
Abstract

Background/Objectives Infant linear-growth faltering remains a major public health issue in low- and middle-income countries and suboptimal breast milk composition may be a local, population-specific risk factor. The relationship between early post-natal breast milk fatty acid (FA) composition and infant growth at 1 and 2 years of age was investigated prospectively in 563 families in Dhaka, Bangladesh. Subjects/Methods A maternal breast milk sample drawn before infant age 6 weeks was analyzed for percentage composition of 26 FAs, and infant length for age Z score (LAZ) was measured longitudinally to infant age 2 years. Individual FAs were tested as predictors of the infant growth outcomes. Results Of 26 tested FAs, %gamma-linolenic acid (%GLA) was mostly significantly associated with increase in LAZ from 6 to 52 weeks ([DELTA]LAZ(52-6w)), and also to 104 weeks. The association was consistent over all breast milk stages with estimated effect size of +0.05 [DELTA]LAZ(52-6w) per 20% change in %GLA (p value = 3 × 10.sup.-6), and stronger for [DELTA]LAZ(104-6w) at +0.06 (p value = 8 × 10.sup.-7), explaining 1% of the outcome variance. Infant serum zinc measurements at 6 and 18 weeks of age were included in adjusted analyses, suggesting at least partial independence of infant zinc levels. The association was strongest in 417/563 (74.1%) families with %GLA Conclusions This study found that %GLA in breast milk was independently associated with infant linear growth, albeit with small effect size, in a predominantly slum-dwelling, low-income, Bangladeshi cohort., Author(s): Josyf C. Mychaleckyj [sup.1] [sup.2], Dadong Zhang [sup.2], Uma Nayak [sup.1] [sup.2], E. Ross Colgate [sup.3], Marya Carmolli [sup.3], Dorothy Dickson [sup.3], Tahmeed Ahmed [sup.4], Masud Alam [sup.4], Beth [...]

Published
2020
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27. Genetic Intratumor Heterogeneity Remodels the Immune Microenvironment and Induces Immune Evasion in Brain Metastasis of Lung Cancer

Author

Wang, Xin, primary, Bai, Hua, additional, Zhang, Jiyang, additional, Wang, Zhijie, additional, Duan, Jianchun, additional, Cai, Hongqing, additional, Cao, Zheng, additional, Lin, Qingtang, additional, Ding, Xiaosheng, additional, Sun, Yiting, additional, Zhang, Wei, additional, Xu, Xiaoya, additional, Chen, Hao, additional, Zhang, Dadong, additional, Feng, Xiaoli, additional, Wan, Jinghai, additional, Zhang, Jianjun, additional, He, Jie, additional, and Wang, Jie, additional

Published
2023
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31. Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy

Author

Wisdom, Amy J., Mowery, Yvonne M., Hong, Cierra S., Himes, Jonathon E., Nabet, Barzin Y., Qin, Xiaodi, Zhang, Dadong, Chen, Lan, Fradin, Hélène, Patel, Rutulkumar, Bassil, Alex M., Muise, Eric S., King, Daniel A., Xu, Eric S., Carpenter, David J., Kent, Collin L., Smythe, Kimberly S., Williams, Nerissa T., Luo, Lixia, Ma, Yan, Alizadeh, Ash A., Owzar, Kouros, Diehn, Maximilian, Bradley, Todd, and Kirsch, David G.

Published
2020
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32. An aberrant NOTCH2-BCR signaling axis in B cells from patients with chronic GVHD

Author

Poe, Jonathan C., Jia, Wei, Su, Hsuan, Anand, Sarah, Rose, Jeremy J., Tata, Prasanthi V., Suthers, Amy N., Jones, Corbin D., Kuan, Pei Fen, Vincent, Benjamin G., Serody, Jonathan S., Horwitz, Mitchell E., Ho, Vincent T., Pavletic, Steven Z., Hakim, Frances T., Owzar, Kouros, Zhang, Dadong, Blazar, Bruce R., Siebel, Christian W., Chao, Nelson J., Maillard, Ivan, and Sarantopoulos, Stefanie

Published
2017
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33. Single-cell landscape analysis unravels molecular programming of the human B cell compartment in chronic GVHD

Author

Poe, Jonathan C., primary, Fang, Jiyuan, additional, Zhang, Dadong, additional, Lee, Marissa R., additional, DiCioccio, Rachel A., additional, Su, Hsuan, additional, Qin, Xiaodi, additional, Zhang, Jennifer Y., additional, Visentin, Jonathan, additional, Bracken, Sonali J., additional, Ho, Vincent T., additional, Wang, Kathy S., additional, Rose, Jeremy J., additional, Pavletic, Steven Z., additional, Hakim, Frances T., additional, Jia, Wei, additional, Suthers, Amy N., additional, Curry-Chisolm, Itaevia M., additional, Horwitz, Mitchell E., additional, Rizzieri, David A., additional, McManigle, William C., additional, Chao, Nelson J., additional, Cardones, Adela R., additional, Xie, Jichun, additional, Owzar, Kouros, additional, and Sarantopoulos, Stefanie, additional

Published
2023
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37. Supplementary Figures 1-9 from The Long Noncoding RNA NEAT1 Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways

Author

Huang, Jianguo, primary, Sachdeva, Mohit, primary, Xu, Eric, primary, Robinson, Timothy J., primary, Luo, Lixia, primary, Ma, Yan, primary, Williams, Nerissa T., primary, Lopez, Omar, primary, Cervia, Lisa D., primary, Yuan, Fan, primary, Qin, Xiaodi, primary, Zhang, Dadong, primary, Owzar, Kouros, primary, Gokgoz, Nalan, primary, Seto, Andrew, primary, Okada, Tomoyo, primary, Singer, Samuel, primary, Andrulis, Irene L., primary, Wunder, Jay S., primary, Lazar, Alexander J., primary, Rubin, Brian P., primary, Pipho, Krista, primary, Mello, Stephano S., primary, Giudice, Jimena, primary, and Kirsch, David G., primary

Published
2023
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39. Supplementary Tables 1-6 from The Long Noncoding RNA NEAT1 Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways

Author

Huang, Jianguo, primary, Sachdeva, Mohit, primary, Xu, Eric, primary, Robinson, Timothy J., primary, Luo, Lixia, primary, Ma, Yan, primary, Williams, Nerissa T., primary, Lopez, Omar, primary, Cervia, Lisa D., primary, Yuan, Fan, primary, Qin, Xiaodi, primary, Zhang, Dadong, primary, Owzar, Kouros, primary, Gokgoz, Nalan, primary, Seto, Andrew, primary, Okada, Tomoyo, primary, Singer, Samuel, primary, Andrulis, Irene L., primary, Wunder, Jay S., primary, Lazar, Alexander J., primary, Rubin, Brian P., primary, Pipho, Krista, primary, Mello, Stephano S., primary, Giudice, Jimena, primary, and Kirsch, David G., primary

Published
2023
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40. Data from The Long Noncoding RNA NEAT1 Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways

Author

Huang, Jianguo, primary, Sachdeva, Mohit, primary, Xu, Eric, primary, Robinson, Timothy J., primary, Luo, Lixia, primary, Ma, Yan, primary, Williams, Nerissa T., primary, Lopez, Omar, primary, Cervia, Lisa D., primary, Yuan, Fan, primary, Qin, Xiaodi, primary, Zhang, Dadong, primary, Owzar, Kouros, primary, Gokgoz, Nalan, primary, Seto, Andrew, primary, Okada, Tomoyo, primary, Singer, Samuel, primary, Andrulis, Irene L., primary, Wunder, Jay S., primary, Lazar, Alexander J., primary, Rubin, Brian P., primary, Pipho, Krista, primary, Mello, Stephano S., primary, Giudice, Jimena, primary, and Kirsch, David G., primary

Published
2023
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42. Supplementary figure S7 from JX06 Selectively Inhibits Pyruvate Dehydrogenase Kinase PDK1 by a Covalent Cysteine Modification

Author

Sun, Wenyi, primary, Xie, Zuoquan, primary, Liu, Yifu, primary, Zhao, Dan, primary, Wu, Zhixiang, primary, Zhang, Dadong, primary, Lv, Hao, primary, Tang, Shuai, primary, Jin, Nan, primary, Jiang, Hualiang, primary, Tan, Minjia, primary, Ding, Jian, primary, Luo, Cheng, primary, Li, Jian, primary, Huang, Min, primary, and Geng, Meiyu, primary

Published
2023
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43. Data from Whole-Exome Sequencing of Radiation-Induced Thymic Lymphoma in Mouse Models Identifies Notch1 Activation as a Driver of p53 Wild-Type Lymphoma

Author

Lee, Chang-Lung, primary, Brock, Kennedy D., primary, Hasapis, Stephanie, primary, Zhang, Dadong, primary, Sibley, Alexander B., primary, Qin, Xiaodi, primary, Gresham, Jeremy S., primary, Caraballo, Isibel, primary, Luo, Lixia, primary, Daniel, Andrea R., primary, Hilton, Matthew J., primary, Owzar, Kouros, primary, and Kirsch, David G., primary

Published
2023
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44. Supplementary Table S2 from JX06 Selectively Inhibits Pyruvate Dehydrogenase Kinase PDK1 by a Covalent Cysteine Modification

Author

Sun, Wenyi, primary, Xie, Zuoquan, primary, Liu, Yifu, primary, Zhao, Dan, primary, Wu, Zhixiang, primary, Zhang, Dadong, primary, Lv, Hao, primary, Tang, Shuai, primary, Jin, Nan, primary, Jiang, Hualiang, primary, Tan, Minjia, primary, Ding, Jian, primary, Luo, Cheng, primary, Li, Jian, primary, Huang, Min, primary, and Geng, Meiyu, primary

Published
2023
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45. Supplementary information from JX06 Selectively Inhibits Pyruvate Dehydrogenase Kinase PDK1 by a Covalent Cysteine Modification

Author

Sun, Wenyi, primary, Xie, Zuoquan, primary, Liu, Yifu, primary, Zhao, Dan, primary, Wu, Zhixiang, primary, Zhang, Dadong, primary, Lv, Hao, primary, Tang, Shuai, primary, Jin, Nan, primary, Jiang, Hualiang, primary, Tan, Minjia, primary, Ding, Jian, primary, Luo, Cheng, primary, Li, Jian, primary, Huang, Min, primary, and Geng, Meiyu, primary

Published
2023
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46. Supplementary Table 1 from Whole-Exome Sequencing of Radiation-Induced Thymic Lymphoma in Mouse Models Identifies Notch1 Activation as a Driver of p53 Wild-Type Lymphoma

Author

Lee, Chang-Lung, primary, Brock, Kennedy D., primary, Hasapis, Stephanie, primary, Zhang, Dadong, primary, Sibley, Alexander B., primary, Qin, Xiaodi, primary, Gresham, Jeremy S., primary, Caraballo, Isibel, primary, Luo, Lixia, primary, Daniel, Andrea R., primary, Hilton, Matthew J., primary, Owzar, Kouros, primary, and Kirsch, David G., primary

Published
2023
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47. Data from JX06 Selectively Inhibits Pyruvate Dehydrogenase Kinase PDK1 by a Covalent Cysteine Modification

Author

Sun, Wenyi, primary, Xie, Zuoquan, primary, Liu, Yifu, primary, Zhao, Dan, primary, Wu, Zhixiang, primary, Zhang, Dadong, primary, Lv, Hao, primary, Tang, Shuai, primary, Jin, Nan, primary, Jiang, Hualiang, primary, Tan, Minjia, primary, Ding, Jian, primary, Luo, Cheng, primary, Li, Jian, primary, Huang, Min, primary, and Geng, Meiyu, primary

Published
2023
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48. Supplementary Table 4 from Whole-Exome Sequencing of Radiation-Induced Thymic Lymphoma in Mouse Models Identifies Notch1 Activation as a Driver of p53 Wild-Type Lymphoma

Author

Lee, Chang-Lung, primary, Brock, Kennedy D., primary, Hasapis, Stephanie, primary, Zhang, Dadong, primary, Sibley, Alexander B., primary, Qin, Xiaodi, primary, Gresham, Jeremy S., primary, Caraballo, Isibel, primary, Luo, Lixia, primary, Daniel, Andrea R., primary, Hilton, Matthew J., primary, Owzar, Kouros, primary, and Kirsch, David G., primary

Published
2023
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49. Supplementary Table 2 from Whole-Exome Sequencing of Radiation-Induced Thymic Lymphoma in Mouse Models Identifies Notch1 Activation as a Driver of p53 Wild-Type Lymphoma

Author

Lee, Chang-Lung, primary, Brock, Kennedy D., primary, Hasapis, Stephanie, primary, Zhang, Dadong, primary, Sibley, Alexander B., primary, Qin, Xiaodi, primary, Gresham, Jeremy S., primary, Caraballo, Isibel, primary, Luo, Lixia, primary, Daniel, Andrea R., primary, Hilton, Matthew J., primary, Owzar, Kouros, primary, and Kirsch, David G., primary

Published
2023
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50. Supplementary Movie S1 from JX06 Selectively Inhibits Pyruvate Dehydrogenase Kinase PDK1 by a Covalent Cysteine Modification

Author

Sun, Wenyi, primary, Xie, Zuoquan, primary, Liu, Yifu, primary, Zhao, Dan, primary, Wu, Zhixiang, primary, Zhang, Dadong, primary, Lv, Hao, primary, Tang, Shuai, primary, Jin, Nan, primary, Jiang, Hualiang, primary, Tan, Minjia, primary, Ding, Jian, primary, Luo, Cheng, primary, Li, Jian, primary, Huang, Min, primary, and Geng, Meiyu, primary

Published
2023
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