Browsing by Author "Zhang, Bo"

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    An atlas of healthy and injured cell states and niches in the human kidney
    (Springer Nature, 2023) Lake, Blue B.; Menon, Rajasree; Winfree, Seth; Hu, Qiwen; Ferreira, Ricardo Melo; Kalhor, Kian; Barwinska, Daria; Otto, Edgar A.; Ferkowicz, Michael; Diep, Dinh; Plongthongkum, Nongluk; Knoten, Amanda; Urata, Sarah; Mariani, Laura H.; Naik, Abhijit S.; Eddy, Sean; Zhang, Bo; Wu, Yan; Salamon, Diane; Williams, James C.; Wang, Xin; Balderrama, Karol S.; Hoover, Paul J.; Murray, Evan; Marshall, Jamie L.; Noel, Teia; Vijayan, Anitha; Hartman, Austin; Chen, Fei; Waikar, Sushrut S.; Rosas, Sylvia E.; Wilson, Francis P.; Palevsky, Paul M.; Kiryluk, Krzysztof; Sedor, John R.; Toto, Robert D.; Parikh, Chirag R.; Kim, Eric H.; Satija, Rahul; Greka, Anna; Macosko, Evan Z.; Kharchenko, Peter V.; Gaut, Joseph P.; Hodgin, Jeffrey B.; KPMP Consortium; Eadon, Michael T.; Dagher, Pierre C.; El-Achkar, Tarek M.; Zhang, Kun; Kretzler, Matthias; Jain, Sanjay; Medicine, School of Medicine
    Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles and interactions within tissue neighbourhoods1. Here we applied multiple single-cell and single-nucleus assays (>400,000 nuclei or cells) and spatial imaging technologies to a broad spectrum of healthy reference kidneys (45 donors) and diseased kidneys (48 patients). This has provided a high-resolution cellular atlas of 51 main cell types, which include rare and previously undescribed cell populations. The multi-omic approach provides detailed transcriptomic profiles, regulatory factors and spatial localizations spanning the entire kidney. We also define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive (successful or maladaptive repair), transitioning and degenerative states. Molecular signatures permitted the localization of these states within injury neighbourhoods using spatial transcriptomics, while large-scale 3D imaging analysis (around 1.2 million neighbourhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways that are relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents a comprehensive benchmark of cellular states, neighbourhoods, outcome-associated signatures and publicly available interactive visualizations.
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    Efficacy and mechanism of Wuzi Yanzong pill on the prevention and treatment of EAE
    (Cell Press, 2023-10-04) Li, Yan-Rong; Zhang, Ruo-Nan; Sun, Rui-Rui; Li, Yan-Yan; Zhang, Bo; Jin, Xiao-Ming; Zhang, Hai-Fei; Xiao, Bao-Guo; Ma, Cun-Gen; Fan, Hui-Jie; Chai, Zhi; Anatomy, Cell Biology and Physiology, School of Medicine
    Objective: Studies have shown that Wuzi Yanzong Pill (WYP) can be used to treat neurological diseases, but its mechanisms for multiple sclerosis (MS) remain unclear. This study aims to determine the effect of WYP on MS in an animal model of experimental autoimmune encephalomyelitis (EAE), and explore its mechanism. To provide theoretical basis for the clinical treatment of MS with WYP. Methods: C57BL/6 female mice were randomly divided into Blank control, EAE control, low dose WYP, medium dose WYP, and high dose WYP groups. One week before model generation, the mice were gavaged with saline (50 mL/kg/d) in Blank control and EAE control groups. The treatment groups was gavaged with different doses of WYP solution (4, 8, or 16 g/kg/d respectively) Clinical scores were recorded daily. Sample collection was conducted on the 14th and 28th days, respectively The expressions of IL-10, IL-17, IL-12, TNF-α and IFN-γ in spleen were detected by ELISA. The expressions of ROCKII, P-MYPT1, TLR4, NF-κB/p65, MCP-1, CCR2 in spleen, brain and spinal cord were detected by Western Blot. The types of macrophages and the contents of intracellular IL-10 and IL-12 were detected by Flow Cytometry. The contents of TNF-α and TLR4 mRNA in the spleen were detected by RT-PCR. Results: WYP treatment improved the clinical score of EAE mice in a significant dose-dependent manner, with the WYP high-dose group showed the most significant improvement in clinical score. Compared with the EAE control group, WYP high dose group had significantly lower levels of IL-17, IFN-γ, ROCKII, P-MYPT1, TLR4, NF-κB/p65, MCP-1, and CCR2 as well as TNF-α and TLR4 mRNA, but increased the number of M2 macrophages and IL-10. Conclusion: WYP treatment relieves clinical symptoms in EAE mice, which may be related to regulate inflammatory pathway and inhibiting expressions of inflammatory cytokines.
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    Macrocephaly and developmental delay caused by missense variants in RAB5C
    (Oxford University Press, 2023) Koop, Klaas; Yuan, Weimin; Tessadori, Federico; Rodriguez-Polanco, Wilmer R.; Grubbs, Jeremy; Zhang, Bo; Osmond, Matt; Graham, Gail; Sawyer, Sarah; Conboy, Erin; Vetrini, Francesco; Treat, Kayla; Płoski, Rafal; Pienkowski, Victor Murcia; Kłosowska, Anna; Fieg, Elizabeth; Krier, Joel; Mallebranche, Coralie; Alban, Ziegler; Aldinger, Kimberly A.; Ritter, Deborah; Macnamara, Ellen; Sullivan, Bonnie; Herriges, John; Alaimo, Joseph T.; Helbig, Catherine; Ellis, Colin A.; van Eyk, Clare; Gecz, Jozef; Farrugia, Daniel; Osei-Owusu, Ikeoluwa; Adès, Lesley; van den Boogaard, Marie-Jose; Fuchs, Sabine; Bakker, Jeroen; Duran, Karen; Dawson, Zachary D.; Lindsey, Anika; Huang, Huiyan; Baldridge, Dustin; Silverman, Gary A.; Grant, Barth D.; Raizen, David; Undiagnosed Diseases Network; van Haaften, Gijs; Pak, Stephen C.; Rehmann, Holger; Schedl, Tim; van Hasselt, Peter; Medical and Molecular Genetics, School of Medicine
    Rab GTPases are important regulators of intracellular vesicular trafficking. RAB5C is a member of the Rab GTPase family that plays an important role in the endocytic pathway, membrane protein recycling and signaling. Here we report on 12 individuals with nine different heterozygous de novo variants in RAB5C. All but one patient with missense variants (n = 9) exhibited macrocephaly, combined with mild-to-moderate developmental delay. Patients with loss of function variants (n = 2) had an apparently more severe clinical phenotype with refractory epilepsy and intellectual disability but a normal head circumference. Four missense variants were investigated experimentally. In vitro biochemical studies revealed that all four variants were damaging, resulting in increased nucleotide exchange rate, attenuated responsivity to guanine exchange factors and heterogeneous effects on interactions with effector proteins. Studies in C. elegans confirmed that all four variants were damaging in vivo and showed defects in endocytic pathway function. The variant heterozygotes displayed phenotypes that were not observed in null heterozygotes, with two shown to be through a dominant negative mechanism. Expression of the human RAB5C variants in zebrafish embryos resulted in defective development, further underscoring the damaging effects of the RAB5C variants. Our combined bioinformatic, in vitro and in vivo experimental studies and clinical data support the association of RAB5C missense variants with a neurodevelopmental disorder characterized by macrocephaly and mild-to-moderate developmental delay through disruption of the endocytic pathway.
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    The chromatin landscape of healthy and injured cell types in the human kidney
    (Springer Nature, 2024-01-10) Gisch, Debora L.; Brennan, Michelle; Lake, Blue B.; Basta, Jeannine; Keller, Mark S.; Ferreira, Ricardo Melo; Akilesh, Shreeram; Ghag, Reetika; Lu, Charles; Cheng, Ying-Hua; Collins, Kimberly S.; Parikh, Samir V.; Rovin, Brad H.; Robbins, Lynn; Stout, Lisa; Conklin, Kimberly Y.; Diep, Dinh; Zhang, Bo; Knoten, Amanda; Barwinska, Daria; Asghari, Mahla; Sabo, Angela R.; Ferkowicz, Michael J.; Sutton, Timothy A.; Kelly, Katherine J.; De Boer, Ian H.; Rosas, Sylvia E.; Kiryluk, Krzysztof; Hodgin, Jeffrey B.; Alakwaa, Fadhl; Winfree, Seth; Jefferson, Nichole; Türkmen, Aydın; Gaut, Joseph P.; Gehlenborg, Nils; Phillips, Carrie L.; El-Achkar, Tarek M.; Dagher, Pierre C.; Hato, Takashi; Zhang, Kun; Himmelfarb, Jonathan; Kretzler, Matthias; Mollah, Shamim; Kidney Precision Medicine Project (KPMP); Jain, Sanjay; Rauchman, Michael; Eadon, Michael T.; Medicine, School of Medicine
    There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. Comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a significant challenge. We measure dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histone modifications to decipher the chromatin landscape and gene regulation of the kidney in reference and adaptive injury states. We establish a spatially-anchored epigenomic atlas to define the kidney's active, silent, and regulatory accessible chromatin regions across the genome. Using this atlas, we note distinct control of adaptive injury in different epithelial cell types. A proximal tubule cell transcription factor network of ELF3, KLF6, and KLF10 regulates the transition between health and injury, while in thick ascending limb cells this transition is regulated by NR2F1. Further, combined perturbation of ELF3, KLF6, and KLF10 distinguishes two adaptive proximal tubular cell subtypes, one of which manifested a repair trajectory after knockout. This atlas will serve as a foundation to facilitate targeted cell-specific therapeutics by reprogramming gene regulatory networks.
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    Wuzi Yanzong Pill relieves CPZ-induced demyelination by improving the microenvironment in the br
    (Elsevier, 2022-12-10) Li, Yan-Rong; Sun, Meng-Ying; Hang, Wei; Xiao, Qi; Fan, Hui-Jie; Jia, Lu; Jin, Xiao-Ming; Zhang, Bo; Xiao, Bao-Guo; Ma, Cun-Gen; Chai, Zhi; Anatomy, Cell Biology and Physiology, School of Medicine
    Ethnopharmacology relevance: Wuzi Yanzong Pill (WYP), a well-known prescription for invigorating the kidney and essence, which is widely used to treat infertility such as oligoasthenospermia. Studies have shown that WYP can be used to treat neurological diseases, but its therapeutic effects and mechanisms for multiple sclerosis (MS) remain unclear. Aim of the study: Based on the establishment of Cuprizone (CPZ)-induced demyelination model, this study determined the effect of WYP on remyelination by detecting changes in the microenvironment of the central nervous system. Materials and methods: C57BL/6 mice were divided into three groups. The CPZ group and CPZ + WYP group were fed with 0.2% CPZ feed, and the control group was fed normal feed, for 6 weeks. At the end of the second week, the CPZ + WYP group was gavaged with WYP solution (16 g/kg/d), and the other two groups were gavaged with normal saline twice a day with an interval of 12 h each time, for 4 weeks. Forced swimming and elevated plus maze were used to detect changes in anxiety and depression before and after treatment. Luxol fast blue staining and the expression of MBP were used to evaluate the demyelination of the brain. Western blot was used to detect the expression of microglia and their subtype markers Iba-1, Arg-1, iNOS, the expression of neurotrophic factors BDNF, GDNF, CNTF, and the expression of oligodendrocyte precursor cells NG2. ELISA detected the content of IL-6, IL-1β, IL-10, TGF-β, BDNF, GDNF, CNTF in the brain. The distribution of Iba-1 in the corpus callosum was observed by immunofluorescence. Results: The results showed that on the basis of improving mood abnormalities and demyelination, WYP reduced the protein content of Iba-1 and iNOS, increased the protein content of Arg-1, and reduce accumulation of microglia in the corpus callosum. In addition, WYP reduced the secretion of IL-6 and IL-1β while promoting the secretion of IL-10 and TGF-β. After WYP intervention treatment, the levels of neurotrophic factors BDNF, GDNF, CNTF increased. Due to the improvement of inflammatory and nutritional environment in the CNS, promoting the proliferation of NG2 oligodendrocyte, increased the expression of MBP, and repairing myelin sheath. Conclusion: Our results indicated that WYP promoted the proliferation and development of oligodendrocytes by improving the CNS microenvironment, effectively alleviating demyelination.