Browsing by Author "Zhou, Yuan"

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    An abnormal bone marrow microenvironment contributes to hematopoietic dysfunction in Fanconi anemia
    (Ferrata Storti Foundation, 2017-06) Zhou, Yuan; He, Yongzheng; Xing, Wen; Zhang, Peng; Shi, Hui; Chen, Shi; Shi, Jun; Bai, Jie; Rhodes, Steven D.; Zhang, Fengqui; Yuan, Jin; Yang, Xianlin; Zhu, Xiaofan; Li, Yan; Hanenberg, Helmut; Xu, Mingjiang; Robertson, Kent A.; Yuan, Weiping; Nalepa, Grzegorz; Cheng, Tao; Clapp, D. Wade; Yang, Feng-Chun; Pediatrics, School of Medicine
    Fanconi anemia is a complex heterogeneous genetic disorder with a high incidence of bone marrow failure, clonal evolution to acute myeloid leukemia and mesenchymal-derived congenital anomalies. Increasing evidence in Fanconi anemia and other genetic disorders points towards an interdependence of skeletal and hematopoietic development, yet the impact of the marrow microenvironment in the pathogenesis of the bone marrow failure in Fanconi anemia remains unclear. Here we demonstrated that mice with double knockout of both Fancc and Fancg genes had decreased bone formation at least partially due to impaired osteoblast differentiation from mesenchymal stem/progenitor cells. Mesenchymal stem/progenitor cells from the double knockout mice showed impaired hematopoietic supportive activity. Mesenchymal stem/progenitor cells of patients with Fanconi anemia exhibited similar cellular deficits, including increased senescence, reduced proliferation, impaired osteoblast differentiation and defective hematopoietic stem/progenitor cell supportive activity. Collectively, these studies provide unique insights into the physiological significance of mesenchymal stem/progenitor cells in supporting the marrow microenvironment, which is potentially of broad relevance in hematopoietic stem cell transplantation.
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    Antimicrobial Stewardship Training for Infectious Diseases Fellows: Program Directors Identify a Curriculum Need
    (Oxford University Press, 2018-04-16) Luther, Vera P.; Shnekendorf, Rachel; Abbo, Lilian M.; Advani, Sonali; Armstrong, Wendy S.; Barsoumian, Alice E.; Beeler, Cole B.; Bystritsky, Rachel; Cherabuddi, Kartikeya; Cohen, Seth; Hamilton, Keith W.; Ince, Dilek; Justo, Julie Ann; Logan, Ashleigh; Lynch, John B., III; Nori, Priya; Ohl, Christopher A.; Patel, Payal K.; Pottinger, Paul S.; Schwartz, Brian S.; Stack, Conor; Zhou, Yuan; Medicine, School of Medicine
    A needs assessment survey of infectious diseases (ID) training program directors identified gaps in educational resources for training and evaluating ID fellows in antimicrobial stewardship. An Infectious Diseases Society of America-sponsored core curriculum was developed to address that need.
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    Base editing in humanized dystrophic mice
    (Elsevier, 2024-04-12) Zhang, Chen; Zhou, Yuan; Han, Renzhi; Pediatrics, School of Medicine
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    Combined loss of Tet1 and Tet2 promotes B-cell, but not myeloid malignancies in mice.
    (Elsevier, 2015-11-24) Zhao, Zhigang; Chen, Li; Dawlaty, Meelad M.; Pan, Feng; Weeks, Ophelia; Zhou, Yuan; Cao, Zeng; Shi, Hui; Wang, Jiapeng; Lin, Li; Chen, Shi; Yuan, Weiping; Qin, Zhaohui; Ni, Hongyu; Nimer, Stephen D.; Yang, Feng-Chun; Jaenisch, Rudolf; Jin, Peng; Xu, Mingjiang; Department of Pediatrics, IU School of Medicine
    TET1/2/3 are methylcytosine dioxygenases that regulate cytosine hydroxymethylation. Tet1/2 are abundantly expressed in HSC/HPCs and are implicated in hematological malignancies. Tet2-deletion in mice causes myeloid malignancies, while Tet1-null mice develop B-cell lymphoma after an extended period of latency. Interestingly, TET1/2 are often concomitantly downregulated in acute B-lymphocytic leukemia. Here, we investigated the overlapping and non-redundant functions of Tet1/2 in HSC maintenance and development of hematological malignancies using Tet1/2 double knockout (DKO) mice. DKO and Tet2−/− HSC/HPCs showed overlapping and unique 5hmC and 5mC profiles, and behaved differently. DKO mice exhibited strikingly decreased incidence and delayed-onset of myeloid malignancies compared to Tet2−/− mice, and in contrast developed lethal B-cell malignancies. Transcriptome analysis of DKO tumors revealed expression changes in many genes dysregulated in human B-cell malignancies, such as LMO2, BCL6 and MYC. These results highlight the critical roles of TET1/2 individually and together via communication in the pathogenesis of hematological malignancies.
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    Computational Analysis of Drought Stress-Associated miRNAs and miRNA Co-Regulation Network in Physcomitrella patens.
    (Elsevier, 2011-04) Wan, Ping; Wu, Jun; Zhou, Yuan; Xiao, Junshu; Feng, Jie; Zhao, Weizhong; Xiang, Shen; Jiang, Guanglong; Chen, Jake Yue; Department of Biohealth Informatics, IU School of Informatics and Computing
    miRNAs are non-coding small RNAs that involve diverse biological processes. Until now, little is known about their roles in plant drought resistance. Physcomitrella patens is highly tolerant to drought; however, it is not clear about the basic biology of the traits that contribute P. patens this important character. In this work, we discovered 16 drought stress-associated miRNA (DsAmR) families in P. patens through computational analysis. Due to the possible discrepancy of expression periods and tissue distributions between potential DsAmRs and their targeting genes, and the existence of false positive results in computational identification, the prediction results should be examined with further experimental validation. We also constructed an miRNA co-regulation network, and identified two network hubs, miR902a-5p and miR414, which may play important roles in regulating drought-resistance traits. We distributed our results through an online database named ppt-miRBase, which can be accessed at http://bioinfor.cnu.edu.cn/ppt_miRBase/index.php. Our methods in finding DsAmR and miRNA co-regulation network showed a new direction for identifying miRNA functions.
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    Defective BVES-mediated feedback control of cAMP in muscular dystrophy
    (Springer Nature, 2023-03-30) Li, Haiwen; Wang, Peipei; Zhang, Chen; Zuo, Yuanbojiao; Zhou, Yuan; Han, Renzhi; Pediatrics, School of Medicine
    Biological processes incorporate feedback mechanisms to enable positive and/or negative regulation. cAMP is an important second messenger involved in many aspects of muscle biology. However, the feedback mechanisms for the cAMP signaling control in skeletal muscle are largely unknown. Here we show that blood vessel epicardial substance (BVES) is a negative regulator of adenylyl cyclase 9 (ADCY9)-mediated cAMP signaling involved in maintaining muscle mass and function. BVES deletion in mice reduces muscle mass and impairs muscle performance, whereas virally delivered BVES expressed in Bves-deficient skeletal muscle reverses these defects. BVES interacts with and negatively regulates ADCY9’s activity. Disruption of BVES-mediated control of cAMP signaling leads to an increased protein kinase A (PKA) signaling cascade, thereby promoting FoxO-mediated ubiquitin proteasome degradation and autophagy initiation. Our study reveals that BVES functions as a negative feedback regulator of ADCY9-cAMP signaling in skeletal muscle, playing an important role in maintaining muscle homeostasis.
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    Evaluation of the Infectious Diseases Society of America’s Core Antimicrobial Stewardship Curriculum for Infectious Diseases Fellows
    (Oxford Academic, 2021-06) Spicer, Jennifer O.; Armstrong, Wendy S.; Schwartz, Brian S.; Abbo, Lilian M.; Advani, Sonali D.; Barsoumian, Alice E.; Beeler, Cole; Bennani, Kenza; Holubar, Marisa; Huang, Misha; Ince, Dilek; Justo, Julie Ann; Lee, Matthew S. L.; Logan, Ashleigh; MacDougall, Conan; Nori, Priya; Ohl, Christopher; Patel, Payal K.; Pottinger, Paul S.; Shnekendorf, Rachel; Stack, Conor; Van Schooneveld, Trevor C.; Willis, Zachary I.; Zhou, Yuan; Luther, Vera P.; Medicine, School of Medicine
    Background Antimicrobial stewardship (AS) programs are required by Centers for Medicare and Medicaid Services and should ideally have infectious diseases (ID) physician involvement; however, only 50% of ID fellowship programs have formal AS curricula. The Infectious Diseases Society of America (IDSA) formed a workgroup to develop a core AS curriculum for ID fellows. Here we study its impact. Methods ID program directors and fellows in 56 fellowship programs were surveyed regarding the content and effectiveness of their AS training before and after implementation of the IDSA curriculum. Fellows’ knowledge was assessed using multiple-choice questions. Fellows completing their first year of fellowship were surveyed before curriculum implementation (“pre-curriculum”) and compared to first-year fellows who complete the curriculum the following year (“post-curriculum”). Results Forty-nine (88%) program directors and 105 (67%) fellows completed the pre-curriculum surveys; 35 (64%) program directors and 79 (50%) fellows completed the post-curriculum surveys. Prior to IDSA curriculum implementation, only 51% of programs had a “formal” curriculum. After implementation, satisfaction with AS training increased among program directors (16% to 68%) and fellows (51% to 68%). Fellows’ confidence increased in 7/10 AS content areas. Knowledge scores improved from a mean of 4.6 to 5.1 correct answers of 9 questions (P = .028). The major hurdle to curriculum implementation was time, both for formal teaching and for e-learning. Conclusions Effective AS training is a critical component of ID fellowship training. The IDSA Core AS Curriculum can enhance AS training, increase fellow confidence, and improve overall satisfaction of fellows and program directors.
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    Hyperactive RAS/PI3-K/MAPK Signaling Cascade in Migration and Adhesion of Nf1 Haploinsufficient Mesenchymal Stem/Progenitor Cells
    (MDPI, 2015-06) Zhou, Yuan; He, Yongzheng; Sharma, Richa; Xing, Wen; Estwick, Selina A.; Wu, Xiaohua; Rhodes, Steven D.; Xu, Mingjiang; Yang, Feng-Chun; Department of Pediatrics, Indiana University School of Medicine
    Neurofibromatosis type 1 (NF1) is an autosomal dominant disease caused by mutations in the NF1 tumor suppressor gene, which affect approximately 1 out of 3000 individuals. Patients with NF1 suffer from a range of malignant and nonmalignant manifestations such as plexiform neurofibromas and skeletal abnormalities. We previously demonstrated that Nf1 haploinsufficiency in mesenchymal stem/progenitor cells (MSPCs) results in impaired osteoblastic differentiation, which may be associated with the skeletal manifestations in NF1 patients. Here we sought to further ascertain the role of Nf1 in modulating the migration and adhesion of MSPCs of the Nf1 haploinsufficient (Nf1+/−) mice. Nf1+/− MSPCs demonstrated increased nuclear-cytoplasmic ratio, increased migration, and increased actin polymerization as compared to wild-type (WT) MSPCs. Additionally, Nf1+/− MSPCs were noted to have significantly enhanced cell adhesion to fibronectin with selective affinity for CH271 with an overexpression of its complimentary receptor, CD49e. Nf1+/− MSPCs also showed hyperactivation of phosphoinositide 3-kinase (PI3-K) and mitogen activated protein kinase (MAPK) signaling pathways when compared to WT MSPCs, which were both significantly reduced in the presence of their pharmacologic inhibitors, LY294002 and PD0325901, respectively. Collectively, our study suggests that both PI3-K and MAPK signaling pathways play a significant role in enhanced migration and adhesion of Nf1 haploinsufficient MSPCs.
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    Integration of evidence across human and model organism studies: A meeting report
    (Wiley, 2021-04-23) Palmer, Rohan H.C.; Johnson, Emma C.; Won, Hyejung; Polimanti, Renato; Kapoor, Manav; Chitre, Apurva; Bogue, Molly A.; Benca-Bachman, Chelsie E.; Parker, Clarissa C.; Verm, Anurag; Reynolds, Timothy; Ernst, Jason; Bray, Michael; Kwon, Soo Bin; Lai, Dongbing; Quach, Bryan C.; Gaddis, Nathan C.; Saba, Laura; Chen, Hao; Hawrylycz, Michael; Zhang, Shan; Zhou, Yuan; Mahaffey, Spencer; Fischer, Christian; Sanchez-Roige, Sandra; Bandrowski, Anita; Lu, Qing; Shen, Li; Philip, Vivek; Gelernter, Joel; Bierut, Laura J.; Hancock, Dana B.; Edenberg, Howard J.; Johnson, Eric O.; Nestler, Eric J.; Barr, Peter B.; Prins, Pjotr; Smith, Desmond J.; Akbarian, Schahram; Thorgeirsson, Thorgeir; Walton, Dave; Baker, Erich; Jacobson, Daniel; Palmer, Abraham A.; Miles, Michael; Chesler, Elissa J.; Emerson, Jake; Agrawal, Arpana; Martone, Maryann; Williams, Robert W.; Medical and Molecular Genetics, School of Medicine
    The National Institute on Drug Abuse and Joint Institute for Biological Sciences at the Oak Ridge National Laboratory hosted a meeting attended by a diverse group of scientists with expertise in substance use disorders (SUDs), computational biology, and FAIR (Findability, Accessibility, Interoperability, and Reusability) data sharing. The meeting's objective was to discuss and evaluate better strategies to integrate genetic, epigenetic, and 'omics data across human and model organisms to achieve deeper mechanistic insight into SUDs. Specific topics were to (a) evaluate the current state of substance use genetics and genomics research and fundamental gaps, (b) identify opportunities and challenges of integration and sharing across species and data types, (c) identify current tools and resources for integration of genetic, epigenetic, and phenotypic data, (d) discuss steps and impediment related to data integration, and (e) outline future steps to support more effective collaboration-particularly between animal model research communities and human genetics and clinical research teams. This review summarizes key facets of this catalytic discussion with a focus on new opportunities and gaps in resources and knowledge on SUDs.
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    Interleukin 8/KC enhances G-CSF induced hematopoietic stem/progenitor cell mobilization in Fancg deficient mice
    (AME Publishing Company, 2014) Li, Yan; Xing, Wen; He, Yong-Zheng; Chen, Shi; Rhodes, Steven D.; Yuan, Jin; Zhou, Yuan; Shi, Jun; Bai, Jie; Zhang, Feng-Kui; Yuan, Wei-Ping; Cheng, Tao; Xu, Ming-Jiang; Yang, Feng-Chun; Department of Pediatrics, IU School of Medicine
    BACKGROUND: Fanconi anemia (FA) is a heterogeneous genetic disorder characterized by a progressive bone marrow aplasia, chromosomal instability, and acquisition of malignancies. Successful hematopoietic cell transplantation (HCT) for FA patients is challenging due to hypersensitivity to DNA alkylating agents and irradiation of FA patients. Early mobilization of autologous stem cells from the bone marrow has been thought to be ideal prior to the onset of bone marrow failure, which often occurs during childhood. However, the markedly decreased response of FA hematopoietic stem cells to granulocyte colony-stimulating factor (G-CSF) is circumventive of this autologous HCT approach. To-date, the mechanism for defective stem cell mobilization in G-CSF treated FA patients remains unclear. METHODS: Fancg heterozygous (Fancg (+/-)) mice utilized in these studies. Student's t-test and one-way ANOVA were used to evaluate statistical differences between WT and Fancg (-/-) cells. Statistical significance was defined as P values less than 0.05. RESULTS: Fancg deficient (Fancg (-/-)) mesenchymal stem/progenitor cells (MSPCs) produce significant lower levels of KC, an interleukin-8 (IL-8) related chemoattractant protein in rodents, as compared to wild type cells. Combinatorial administration of KC and G-CSF significantly increased the mobilization of hematopoietic stem/progenitor cells (HSPCs) in Fancg (-/-) mice. CONCLUSIONS: In summary, our results suggest that KC/IL-8 could be proved useful in the synergistic mobilization of FA HSPCs in combination with G-CSF.