Browsing by Author "Yang, Fan"

Now showing 1 - 8 of 8
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    Cardiac Sca-1+ cells are not intrinsic stem cells for myocardial development, renewal and repair
    (American Heart Association, 2018-12-18) Zhang, Lu; Sultana, Nishat; Yan, Jianyun; Yang, Fan; Chen, Fuxue; Chepurko, Elena; Yang, Feng-Chun; Du, Qinghua; Zangi, Lior; Xu, Mingjiang; Bu, Lei; Cai, Chen-Leng; Pediatrics, School of Medicine
    Background: For over a decade, Sca-1+ cells within the mouse heart have been widely recognized as a stem cell population with multipotency that can give rise to cardiomyocytes, endothelial cells and smooth muscle cells in vitro and after cardiac grafting. However, the developmental origin and authentic nature of these cells remain elusive. Methods: Here, we used a series of high-fidelity genetic mouse models to characterize the identity and regenerative potential of cardiac resident Sca-1+ cells. Results: With these novel genetic mouse models, we found that Sca-1 does not label cardiac precursor cells during early embryonic heart formation. Postnatal cardiac resident Sca-1+ cells are in fact a pure endothelial cell population. They retain endothelial properties and exhibit minimal cardiomyogenic potential during development, normal aging and upon ischemic injury. Conclusions: Our study provides definitive insights into the nature of cardiac resident Sca-1+ cells. The observations challenge the current dogma that cardiac resident Sca-1+ cells are intrinsic stem cells for myocardial development, renewal and repair and suggest that the mechanisms of transplanted Sca-1+ cells in heart repair need to be reassessed.
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    Development and interpretation of a pathomics-based model for the prediction of microsatellite instability in Colorectal Cancer
    (Ivyspring International Publisher, 2020-09-02) Cao, Rui; Yang, Fan; Ma, Si-Cong; Liu, Li; Zhao, Yu; Li, Yan; Wu, De-Hua; Wang, Tongxin; Lu, Wei-Jia; Cai, Wei-Jing; Zhu, Hong-Bo; Guo, Xue-Jun; Lu, Yu-Wen; Kuang, Jun-Jie; Huan, Wen-Jing; Tang, Wei-Min; Huang, Kun; Huang, Junzhou; Yao, Jianhua; Dong, Zhong-Yi; Biostatistics, School of Public Health
    Microsatellite instability (MSI) has been approved as a pan-cancer biomarker for immune checkpoint blockade (ICB) therapy. However, current MSI identification methods are not available for all patients. We proposed an ensemble multiple instance deep learning model to predict microsatellite status based on histopathology images, and interpreted the pathomics-based model with multi-omics correlation. Methods: Two cohorts of patients were collected, including 429 from The Cancer Genome Atlas (TCGA-COAD) and 785 from an Asian colorectal cancer (CRC) cohort (Asian-CRC). We established the pathomics model, named Ensembled Patch Likelihood Aggregation (EPLA), based on two consecutive stages: patch-level prediction and WSI-level prediction. The initial model was developed and validated in TCGA-COAD, and then generalized in Asian-CRC through transfer learning. The pathological signatures extracted from the model were analyzed with genomic and transcriptomic profiles for model interpretation. Results: The EPLA model achieved an area-under-the-curve (AUC) of 0.8848 (95% CI: 0.8185-0.9512) in the TCGA-COAD test set and an AUC of 0.8504 (95% CI: 0.7591-0.9323) in the external validation set Asian-CRC after transfer learning. Notably, EPLA captured the relationship between pathological phenotype of poor differentiation and MSI (P < 0.001). Furthermore, the five pathological imaging signatures identified from the EPLA model were associated with mutation burden and DNA damage repair related genotype in the genomic profiles, and antitumor immunity activated pathway in the transcriptomic profiles. Conclusions: Our pathomics-based deep learning model can effectively predict MSI from histopathology images and is transferable to a new patient cohort. The interpretability of our model by association with pathological, genomic and transcriptomic phenotypes lays the foundation for prospective clinical trials of the application of this artificial intelligence (AI) platform in ICB therapy.
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    Investigation of the Interaction between Nafion Ionomer and Surface Functionalized Carbon Black Using Both Ultrasmall Angle X-ray Scattering and Cryo-TEM
    (ACS, 2017-01) Yang, Fan; Xin, Le; Uzunoglu, Aytekin; Qiu, Yang; Stanciu, Lia; Ilavsky, Jan; Li, Wenzhen; Xie, Jian; Mechanical Engineering, School of Engineering and Technology
    In making a catalyst ink, the interactions between Nafion ionomer and catalyst support are the key factors that directly affect both ionic conductivity and electronic conductivity of the catalyst layer in a membrane electrode assembly. One of the major aims of this investigation is to understand the behavior of the catalyst support, Vulcan XC-72 (XC-72) aggregates, in the existence of the Nafion ionomer in a catalyst ink to fill the knowledge gap of the interaction of these components. The dispersion of catalyst ink depends not only on the solvent but also on the interaction of Nafion and carbon particles in the ink. The interaction of Nafion ionomer particles and XC-72 catalyst aggregates in liquid media was studied using ultrasmall-angle X-ray scattering and cryogenic TEM techniques. Carbon black (XC-72) and functionalized carbon black systems were introduced to study the interaction behaviors. A multiple curve fitting was used to extract the particle size and size distribution from scattering data. The results suggest that the particle size and size distribution of each system changed significantly in Nafion + XC-72 system, Nafion + NH2-XC72 system, and Nafion + SO3H-XC-72 system, which indicates that an interaction among these components (i.e., ionomer particles and XC-72 aggregates) exists. The cryogenic TEM, which allows for the observation the size of particles in a liquid, was used to validate the scattering results and shows excellent agreement.
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    Novel Myh11 Dual Reporter Mouse Model Provides Definitive Labeling and Identification of Smooth Muscle Cells—Brief Report
    (AHA, 2021-02) Ruan, Jian; Zhang, Lu; Hu, Donghua; Qu, Xianghu; Yang, Fan; Chen, Fuxue; He, Xiangqin; Shen, Jian; Dong, Kunzhe; Sweet, Megan; Sanchez, Christina; Li, Deqiang; Shou, Weinian; Zhou, Jiliang; Cai, Chen-Leng; Pediatrics, School of Medicine
    Objective: Myh11 encodes a myosin heavy chain protein that is specifically expressed in smooth muscle cells (SMCs) and is important for maintaining vascular wall stability. The goal of this study is to generate a Myh11 dual reporter mouse line for definitive visualization of MYH11+ SMCs in vivo. Approach and Results: We generated a Myh11 knock-in mouse model by inserting LoxP-nlacZ-4XpolyA-LoxP-H2B-GFP-polyA-FRT-Neo-FRT reporter cassette into the Myh11 gene locus. The nuclear (n) lacZ-4XpolyA cassette is flanked by 2 LoxP sites followed by H2B-GFP (histone 2B fused green fluorescent protein). Upon Cre-mediated recombination, nlacZ-stop cassette is removed thereby permitting nucleus localized H2B-GFP expression. Expression of the nuclear localized lacZ or H2B-GFP is under control of the endogenous Myh11 promoter. Nuclear lacZ was expressed specifically in SMCs at embryonic and adult stages. Following germline Cre-mediated deletion of nuclear lacZ, H2B-GFP was specifically expressed in the nuclei of SMCs. Comparison of nuclear lacZ expression with Wnt1Cre and Mef2cCre mediated-H2B-GFP expression revealed heterogenous origins of SMCs from neural crest and second heart field in the great arteries and coronary vessels adjacent to aortic root. Conclusions: The Myh11 knock-in dual reporter mouse model offers an exceptional genetic tool to visualize and trace the origins of SMCs in mice.
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    Polybenzimidazole (PBI) Functionalized Nanographene as Highly Stable Catalyst Support for Polymer Electrolyte Membrane Fuel Cells (PEMFCs)
    (ECS, 2016) Xin, Le; Yang, Fan; Qiu, Yang; Uzunoglu, Aytekin; Rockward, Tommy; Borup, Rodney L.; Stanciu, Lia A.; Li, Wenzhen; Xie, Jian; Department of Mechanical Engineering, School of Engineering and Technology
    Nanoscale graphenes were used as cathode catalyst supports in proton exchange membrane fuel cells (PEMFCs). Surface-initiated polymerization that covalently bonds polybenzimidazole (PBI) polymer on the surface of graphene supports enables the uniform distribution of the Pt nanoparticles, as well as allows the sealing of the unterminated carbon bonds usually present on the edge of graphene from the chemical reduction of graphene oxide. The nanographene effectively shortens the length of channels and pores for O2 diffusion/water dissipation and significantly increases the primary pore volume. Further addition of p-phenyl sulfonic functional graphitic carbon particles as spacers, increases the specific volume of the secondary pores and greatly improves O2 mass transport within the catalyst layers. The developed composite cathode catalyst of Pt/PBI-nanographene (50 wt%) + SO3H-graphitic carbon black demonstrates a higher beginning of life (BOL) PEMFC performance as compared to both Pt/PBI-nanographene (50 wt%) and Pt/PBI-graphene (50 wt%) + SO3H-graphitic carbon black (GCB). Accelerated stress tests show excellent support durability compared to that of traditional Pt/Vulcan XC72 catalysts, when subjected to 10,000 cycles from 1.0 V to 1.5 V. This study suggests the promise of using PBI-nanographene + SO3H-GCB hybrid supports in fuel cells to achieve the 2020 DOE targets for transportation applications.
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    Rtr1 is a dual specificity phosphatase that dephosphorylates Tyr1 and Ser5 on the RNA Polymerase II CTD
    (Elsevier, 2014-08-12) Hsu, Peter L.; Yang, Fan; Smith-Kinnaman, Whitney; Yang, Wen; Song, Jae-Eun; Mosley, Amber L.; Varani, Gabriele; Department of Biochemistry and Molecular Biology, IU School of Medicine
    The phosphorylation state of heptapeptide repeats within the C-terminal domain (CTD) of the largest subunit of RNA Polymerase II (PolII) controls the transcription cycle and is maintained by the competing action of kinases and phosphatases. Rtr1 was recently proposed to be the enzyme responsible for the transition of PolII into the elongation and termination phases of transcription by removing the phosphate marker on Serine 5, but this attribution was questioned by the apparent lack of enzymatic activity. Here we demonstrate that Rtr1 is a phosphatase of new structure that is auto-inhibited by its own C-terminus. The enzymatic activity of the protein in vitro is functionally important in vivo as well: a single amino acid mutation that reduces activity leads to the same phenotype in vivo as deletion of the protein-coding gene from yeast. Surprisingly, Rtr1 dephosphorylates not only Serine 5 on the CTD, but also the newly described anti-termination Tyrosine 1 marker, supporting the hypothesis that Rtr1 and its homologs promote the transition from transcription to termination.
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    STAT5 programs a distinct subset of GM-CSF-producing T helper cells that is essential for autoimmune neuroinflammation
    (Nature Publishing Group, 2014-12) Sheng, Wanqiang; Yang, Fan; Zhou, Yi; Yang, Henry; Low, Pey Yng; Kemeny, David Michael; Tan, Patrick; Moh, Akira; Kaplan, Mark H.; Zhang, Yongliang; Fu, Xin-Yuan; Department of Pediatrics, IU School of Medicine
    T helper (TH)-cell subsets, such as TH1 and TH17, mediate inflammation in both peripheral tissues and central nervous system. Here we show that STAT5 is required for T helper-cell pathogenicity in autoimmune neuroinflammation but not in experimental colitis. Although STAT5 promotes regulatory T cell generation and immune suppression, loss of STAT5 in CD4+ T cells resulted in diminished development of experimental autoimmune encephalomyelitis (EAE), a mouse model of multiple sclerosis. Our results showed that loss of encephalitogenic activity of STAT5-deficient autoreactive CD4+ T cells was independent of IFN-γ or interleukin 17 (IL-17) production, but was due to the impaired expression of granulocyte-macrophage colony-stimulating factor (GM-CSF), a crucial mediator of T-cell pathogenicity. We further showed that IL-7-activated STAT5 promotes the generation of GM-CSF-producing CD4+ T cells, which were preferentially able to induce more severe EAE than TH17 or TH1 cells. Consistent with GM-CSF-producing cells being a distinct subset of TH cells, the differentiation program of these cells was distinct from that of TH17 or TH1 cells. We further found that IL-3 was secreted in a similar pattern as GM-CSF in this subset of TH cells. In conclusion, the IL-7-STAT5 axis promotes the generation of GM-CSF/IL-3-producing TH cells. These cells display a distinct transcriptional profile and may represent a novel subset of T helper cells which we designate as TH-GM.
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    Study of catalysts with high stability for proton exchange membrane fuel cells
    (2015-08) Yang, Fan; Xie, Jian
    The innovation and investigation of catalysts in proton exchange membrane fuel cells are included in this thesis. In the first part of this work, stability of the catalyst support of PEMFC catalyst is investigated. Nanoscale platinum particles were loaded on two different kinds of carbon supports, nano graphene sheets and functionalized carbon black/graphene hybrid were developed by the liquid phase reaction. The crystal structure of two kinds of catalysts was characterized by X-ray diffractometer (XRD). The morphology and particle size were characterized by scanning electron microscope (SEM) and transmission electron microscope (TEM). Pt loading was measured by thermal gravimetric analysis (TGA). The Brunauer, Emmett and Teller (BET) method was applied to test the surface area of the catalysts. The electrochemical surface area (ECSA) and mass activity during oxygen reduction reaction (ORR) process for two kinds of catalyst were tested by cyclic voltammetry method under different conditions. The stability of the catalysts were tested by accelerated durability test (ADT). The results show that although the mass activity of Pt/graphene is much lower, the stability of it is much better than that of the commercial catalyst. After adding functionalized carbon black (FCB) as spacer, the stability of the catalyst is preserved and at the meantime, the mass activity becomes higher than 20% Pt/XC72 catalyst. The lower mass activity of both catalysts are due to the limitation of the electrolyte diffusion into the carbon support because of the aggregation nature of graphene nano-sheets. After introducing functional carbon black as spacer, the mass activity and ECSA increased dramatically which proved that FCB can be applied to prevent the restacking of graphene and hence solved the diffusion problem. In the meantime, the durability was still keeping the same as Pt/graphene catalyst. In the second part of the work, the restacking problem was solved by introducing FCB as spacers between functionalized graphene nanosheets. The same measurement was applied to test the electrochemical performance of Pt/FCB/FG catalyst. The new catalyst showed a higher mass activity compared to Pt/graphene catalyst which meant the restacking problem was partially solved. The durability of the Pt/FCB/FG catalyst was still excellent.