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  • 1
    Online Resource
    Online Resource
    GPCards: An integrated database of genotype–phenotype correlations in human genetic diseases
    Elsevier BV ; 2021
    In:  Computational and Structural Biotechnology Journal Vol. 19 ( 2021), p. 1603-1611
    Details
    In: Computational and Structural Biotechnology Journal, Elsevier BV, Vol. 19 ( 2021), p. 1603-1611
    Type of Medium: Online Resource
    ISSN: 2001-0370
    URL: Article
    DOI: 10.1016/j.csbj.2021.03.011
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2021
    detail.hit.zdb_id: 2694435-2
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  • 2
    Online Resource
    Online Resource
    Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders
    Oxford University Press (OUP) ; 2019
    In:  National Science Review Vol. 6, No. 6 ( 2019-11-01), p. 1201-1222
    Details
    In: National Science Review, Oxford University Press (OUP), Vol. 6, No. 6 ( 2019-11-01), p. 1201-1222
    Abstract: Human genetic adaptation to high altitudes ( & gt;2500 m) has been extensively studied over the last few years, but few functional adaptive genetic variants have been identified, largely owing to the lack of deep-genome sequencing data available to previous studies. Here, we build a list of putative adaptive variants, including 63 missense, 7 loss-of-function, 1,298 evolutionarily conserved variants and 509 expression quantitative traits loci. Notably, the top signal of selection is located in TMEM247, a transmembrane protein-coding gene. The Tibetan version of TMEM247 harbors one high-frequency (76.3%) missense variant, rs116983452 (c.248C  & gt; T; p.Ala83Val), with the T allele derived from archaic ancestry and carried by & gt;94% of Tibetans but absent or in low frequencies ( & lt;3%) in non-Tibetan populations. The rs116983452-T is strongly and positively correlated with altitude and significantly associated with reduced hemoglobin concentration (p = 5.78 × 10−5), red blood cell count (p = 5.72 × 10−7) and hematocrit (p = 2.57 × 10−6). In particular, TMEM247-rs116983452 shows greater effect size and better predicts the phenotypic outcome than any EPAS1 variants in association with adaptive traits in Tibetans. Modeling the interaction between TMEM247-rs116983452 and EPAS1 variants indicates weak but statistically significant epistatic effects. Our results support that multiple variants may jointly deliver the fitness of the Tibetans on the plateau, where a complex model is needed to elucidate the adaptive evolution mechanism.
    Type of Medium: Online Resource
    ISSN: 2095-5138 , 2053-714X
    URL: Article
    DOI: 10.1093/nsr/nwz108
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2745465-4
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  • 3
    Online Resource
    Online Resource
    Long-term ozone exposure is negatively associated with estimated glomerular filtration rate in Chinese middle-aged and elderly adults
    Elsevier BV ; 2023
    In:  Chemosphere Vol. 341 ( 2023-11), p. 140040-
    Details
    In: Chemosphere, Elsevier BV, Vol. 341 ( 2023-11), p. 140040-
    Type of Medium: Online Resource
    ISSN: 0045-6535
    URL: Article
    DOI: 10.1016/j.chemosphere.2023.140040
    RVK:
    AR 10100
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 1496851-4
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  • 4
    Online Resource
    Online Resource
    CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells
    Springer Science and Business Media LLC ; 2021
    In:  Nature Communications Vol. 12, No. 1 ( 2021-10-01)
    Details
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-10-01)
    Abstract: Regulatory T (Treg) cells are one of the major immunosuppressive cell types in cancer and a potential target for immunotherapy, but targeting tumor-infiltrating (TI) Treg cells has been challenging. Here, using single-cell RNA sequencing of immune cells from renal clear cell carcinoma (ccRCC) patients, we identify two distinct transcriptional fates for TI Treg cells, Fate-1 and Fate-2. The Fate-1 signature is associated with a poorer prognosis in ccRCC and several other solid cancers. CD177, a cell surface protein normally expressed on neutrophil, is specifically expressed on Fate-1 TI Treg cells in several solid cancer types, but not on other TI or peripheral Treg cells. Mechanistically, blocking CD177 reduces the suppressive activity of Treg cells in vitro, while Treg-specific deletion of Cd177 leads to decreased tumor growth and reduced TI Treg frequency in mice. Our results thus uncover a functional CD177 + TI Treg population that may serve as a target for TI Treg-specific immunotherapy.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    URL: Article
    DOI: 10.1038/s41467-021-26091-4
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2553671-0
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  • 5
    Online Resource
    Online Resource
    Spraying exogenous hormones alleviate impact of weak-light on yield by improving leaf carbon and nitrogen metabolism in fresh waxy maize
    Frontiers Media SA ; 2023
    In:  Frontiers in Plant Science Vol. 14 ( 2023-6-20)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 14 ( 2023-6-20)
    Abstract: Insufficient light during the growth periods has become one of the main factors restricting maize yield with global climate change. Exogenous hormones application is a feasible measure to alleviate abiotic stresses on crop productivity. In this study, a field trial was conducted to investigate the effects of spraying exogenous hormones on yield, dry matter (DM) and nitrogen (N) accumulation, leaf carbon and N metabolism of fresh waxy maize under weak-light stress in 2021 and 2022. Five treatments including natural light (CK), weak-light after pollination (Z), spraying water (ZP1), exogenous Phytase Q9 (ZP2) and 6-benzyladenine (ZP3) under weak-light after pollination were set up using two hybrids suyunuo5 (SYN5) and jingkenuo2000 (JKN2000). Results showed that weak-light stress significantly reduced the average fresh ear yield (49.8%), fresh grain yield (47.9%), DM (53.3%) and N accumulation (59.9%), and increased grain moisture content. The net photosynthetic rate (Pn), transpiration rate (Tr) of ear leaf after pollination decreased under Z. Furthermore, weak-light decreased the activities of RuBPCase and PEPCase, nitrate reductase (NR), glutamine synthetase (GS), glutamate synthase (GOGAT), superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) in ear leaves, and increased malondialdehyde (MDA) accumulation. And the decrease was greater on JKN2000. While ZP2 and ZP3 treatments increased the fresh ear yield (17.8%, 25.3%), fresh grain yield (17.2%, 29.5%), DM (35.8%, 44.6%) and N (42.5%, 52.4%) accumulation, and decreased grain moisture content compared with Z. The Pn, Tr increased under ZP2 and ZP3. Moreover, the ZP2 and ZP3 treatments improved the activities of RuBPCase, PEPCase; NR, GS, GOGAT; SOD, CAT, POD in ear leaves, and decreased MDA content during grain filling stage. The results also showed the mitigative effect of ZP3 was greater than ZP2, and the improvement effect was more significant on JKN2000.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    DOI: 10.3389/fpls.2023.1220827
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 6
    Online Resource
    Online Resource
    Genomic diversity and post-admixture adaptation in the Uyghurs
    Oxford University Press (OUP) ; 2022
    In:  National Science Review Vol. 9, No. 3 ( 2022-03-25)
    Details
    In: National Science Review, Oxford University Press (OUP), Vol. 9, No. 3 ( 2022-03-25)
    Abstract: Population admixture results in genome-wide combinations of genetic variants derived from different ancestral populations of distinct ancestry, thus providing a unique opportunity for understanding the genetic determinants of phenotypic variation in humans. Here, we used whole-genome sequencing of 92 individuals with high coverage (30–60×) to systematically investigate genomic diversity in the Uyghurs living in Xinjiang, China (XJU), an admixed population of both European-like and East-Asian-like ancestry. The XJU population shows greater genetic diversity, especially a higher proportion of rare variants, compared with their ancestral source populations, corresponding to greater phenotypic diversity of XJU. Admixture-induced functional variants in EDAR were associated with the diversity of facial morphology in XJU. Interestingly, the interaction of functional variants between SLC24A5 and OCA2 likely influences the diversity of skin pigmentation. Notably, selection has seemingly been relaxed or canceled in several genes with significantly biased ancestry, such as HERC2–OCA2. Moreover, signatures of post-admixture adaptation in XJU were identified, including genes related to metabolism (e.g. CYP2D6), digestion (e.g. COL11A1), olfactory perception (e.g. ANO2) and immunity (e.g. HLA). Our results demonstrated population admixture as a driving force, locally or globally, in shaping human genetic and phenotypic diversity as well as in adaptive evolution.
    Type of Medium: Online Resource
    ISSN: 2095-5138 , 2053-714X
    URL: Article
    DOI: 10.1093/nsr/nwab124
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2745465-4
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  • 7
    Online Resource
    Online Resource
    Low level laser therapy promotes bone regeneration by coupling angiogenesis and osteogenesis
    Springer Science and Business Media LLC ; 2021
    In:  Stem Cell Research & Therapy Vol. 12, No. 1 ( 2021-12)
    Details
    In: Stem Cell Research & Therapy, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-12)
    Abstract: Bone tissue engineering is a new concept bringing hope for the repair of large bone defects, which remains a major clinical challenge. The formation of vascularized bone is key for bone tissue engineering. Growth of specialized blood vessels termed type H is associated with bone formation. In vivo and in vitro studies have shown that low level laser therapy (LLLT) promotes angiogenesis, fracture healing, and osteogenic differentiation of stem cells by increasing reactive oxygen species (ROS). However, whether LLLT can couple angiogenesis and osteogenesis, and the underlying mechanisms during bone formation, remains largely unknown. Methods Mouse bone marrow mesenchymal stem cells (BMSCs) combined with biphasic calcium phosphate (BCP) grafts were implanted into C57BL/6 mice to evaluate the effects of LLLT on the specialized vessel subtypes and bone regeneration in vivo. Furthermore, human BMSCs and human umbilical vein endothelial cells (HUVECs) were co-cultured in vitro. The effects of LLLT on cell proliferation, angiogenesis, and osteogenesis were assessed. Results LLLT promoted the formation of blood vessels, collagen fibers, and bone tissue and also increased CD31 hi EMCN hi -expressing type H vessels in mBMSC/BCP grafts implanted in mice. LLLT significantly increased both osteogenesis and angiogenesis, as well as related gene expression (HIF-1α, VEGF, TGF-β) of grafts in vivo and of co-cultured BMSCs/HUVECs in vitro. An increase or decrease of ROS induced by H 2 O 2 or Vitamin C, respectively, resulted in an increase or decrease of HIF-1α, and a subsequent increase and decrease of VEGF and TGF-β in the co-culture system. The ROS accumulation induced by LLLT in the co-culture system was significantly decreased when HIF-1α was inhibited with DMBPA and was followed by decreased expression of VEGF and TGF-β. Conclusions LLLT enhanced vascularized bone regeneration by coupling angiogenesis and osteogenesis. ROS/HIF-1α was necessary for these effects of LLLT. LLLT triggered a ROS-dependent increase of HIF-1α, VEGF, and TGF-β and resulted in subsequent formation of type H vessels and osteogenic differentiation of mesenchymal stem cells. As ROS also was a target of HIF-1α, there may be a positive feedback loop between ROS and HIF-1α, which further amplified HIF-1α induction via the LLLT-mediated ROS increase. This study provided new insight into the effects of LLLT on vascularization and bone regeneration in bone tissue engineering.
    Type of Medium: Online Resource
    ISSN: 1757-6512
    URL: Article
    DOI: 10.1186/s13287-021-02493-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2548671-8
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  • 8
    Online Resource
    Online Resource
    PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations
    Springer Science and Business Media LLC ; 2019
    In:  Genome Biology Vol. 20, No. 1 ( 2019-12)
    Details
    In: Genome Biology, Springer Science and Business Media LLC, Vol. 20, No. 1 ( 2019-12)
    Abstract: Despite the tremendous growth of the DNA sequencing data in the last decade, our understanding of the human genome is still in its infancy. To understand the implications of genetic variants in the light of population genetics and molecular evolution, we developed a database, PGG .SNV ( https://www.pggsnv.org ), which gives much higher weight to previously under-investigated indigenous populations in Asia. PGG .SNV archives 265 million SNVs across 220,147 present-day genomes and 1018 ancient genomes, including 1009 newly sequenced genomes, representing 977 global populations. Moreover, estimation of population genetic diversity and evolutionary parameters is available in PGG .SNV, a unique feature compared with other databases.
    Type of Medium: Online Resource
    ISSN: 1474-760X
    URL: Article
    DOI: 10.1186/s13059-019-1838-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
    detail.hit.zdb_id: 2040529-7
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  • 9
    Online Resource
    Online Resource
    Peripheral immune mapping and multi-omics analysis in Pd -1 inhibitor–induced myocarditis
    Oxford University Press (OUP) ; 2023
    In:  Journal of Leukocyte Biology Vol. 114, No. 2 ( 2023-07-27), p. 164-179
    Details
    In: Journal of Leukocyte Biology, Oxford University Press (OUP), Vol. 114, No. 2 ( 2023-07-27), p. 164-179
    Abstract: More immune-related adverse events (irAEs) have emerged along with increased immune checkpoint inhibitor (ICI) treatment. ICI-induced myocarditis is a rare type of irAE with early onset, rapid progression, and high mortality. Its specific pathophysiological mechanism is not fully understood. In total, 46 patients with tumors and 16 patients with ICI-induced myocarditis were included. We performed single-cell RNA sequencing on CD3 + T cells, flow cytometry, proteomics, and lipidomics to improve our understanding of the disease. First, we demonstrate the clinical features of patients with PD-1 inhibitor–induced myocarditis. We then identified 18 subsets of T cells using single-cell RNA sequencing and performed comparative analysis and further verification. The composition of T cells in the peripheral blood of patients has changed remarkably. Compared with non-irAE patients, effector T cells were increased in irAE patients, while naive T cells, γδ T cells, and mucosal-associated invariant T cell cluster cells were decreased. Besides, reduced γδ T cells characterized with effector functions, increased natural killer T cells with high levels of FCER1G in patients may suggest an association with disease development. Meanwhile, the peripheral inflammatory response was exacerbated in patients, accompanied by upregulation of exocytosis as well as increased levels of multiple lipids. We provide a comprehensive overview of the composition, gene profiles, and pathway signatures of CD3+ T cells driven by PD-1 inhibitor–induced myocarditis, as well as illustrate clinical features and multi-omic characteristics, providing a unique perspective on disease progression and therapy in clinical practice.
    Type of Medium: Online Resource
    ISSN: 1938-3673
    URL: Article
    DOI: 10.1093/jleuko/qiad056
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2026833-6
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  • 10
    Online Resource
    Online Resource
    Genetic Origins and Sex-Biased Admixture of the Huis
    Oxford University Press (OUP) ; 2021
    In:  Molecular Biology and Evolution Vol. 38, No. 9 ( 2021-08-23), p. 3804-3819
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 38, No. 9 ( 2021-08-23), p. 3804-3819
    Abstract: The Hui people are unique among Chinese ethnic minorities in that they speak the same language as Han Chinese (HAN) but practice Islam. However, as the second-largest minority group in China numbering well over 10 million, the Huis are under-represented in both global and regional genomic studies. Here, we present the first whole-genome sequencing effort of 234 Hui individuals (NXH) aged over 60 who have been living in Ningxia, where the Huis are mostly concentrated. NXH are genetically more similar to East Asian than to any other global populations. In particular, the genetic differentiation between NXH and HAN (FST = 0.0015) is only slightly larger than that between northern and southern HAN (FST = 0.0010), largely attributed to the western ancestry in NXH (∼10%). Highly differentiated functional variants between NXH and HAN were identified in genes associated with skin pigmentation (e.g., SLC24A5), facial morphology (e.g., EDAR), and lipid metabolism (e.g., ABCG8). The Huis are also distinct from other Muslim groups such as the Uyghurs (FST = 0.0187), especially, NXH derived much less western ancestry (∼10%) compared with the Uyghurs (∼50%). Modeling admixture history indicated that NXH experienced an episode of two-wave admixture. An ancient admixture occurred ∼1,025 years ago, reflecting the intensive west–east contacts during the late Tang Dynasty, and the Five Dynasties and Ten Kingdoms period. A recent admixture occurred ∼500 years ago, corresponding to the Ming Dynasty. Notably, we identified considerable sex-biased admixture, that is, excess of western males and eastern females contributing to the NXH gene pool. The origins and the genomic diversity of the Hui people imply the complex history of contacts between western and eastern Eurasians.
    Type of Medium: Online Resource
    ISSN: 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msab158
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2024221-9
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