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  1. Article ; Online: Explore the dominant factor in prime editing via a view of DNA processing

    Zhimeng Xu / Dacheng Ma / Houzhen Su / Xiaodong Jia / Yinqing Li / Yinying Lu / Zhen Xie

    Synthetic and Systems Biotechnology, Vol 8, Iss 3, Pp 371-

    2023  Volume 377

    Abstract: Prime editing is a revolutionary gene-editing method that is capable of introducing insertions, deletions and base substitutions into the genome. However, the editing efficiency of Prime Editor (PE) is limited by the DNA repair process. Here, we show ... ...

    Abstract Prime editing is a revolutionary gene-editing method that is capable of introducing insertions, deletions and base substitutions into the genome. However, the editing efficiency of Prime Editor (PE) is limited by the DNA repair process. Here, we show that overexpression of the flap structure-specific endonuclease 1 (FEN1) and the DNA ligase 1 (LIG1) increases the efficiency of prime editing, which is similar to the dominant negative mutL homolog 1 (MLH1dn). In addition, MLH1 is still the dominant factor over FEN1 and LIG1 in prime editing. Our results help to further understand the relationship of proteins involved in prime editing and envisage future directions for the development of PE.
    Keywords Biotechnology ; TP248.13-248.65 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-09-01T00:00:00Z
    Publisher KeAi Communications Co., Ltd.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Reviewing immunopathology characteristics of SARS-CoV-2 for cancer entwisted with SARS-CoV-2

    Hongyan Li / Wanting Lu / Yinyin Li / Yinying Lu / Fei Li

    SAGE Open Medicine, Vol

    2021  Volume 9

    Abstract: In December 2019, the outbreak of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), infection that started in Wuhan, Hubei Province, China, has spread to all world. Based on the accumulated data and knowledge on the ... ...

    Abstract In December 2019, the outbreak of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), infection that started in Wuhan, Hubei Province, China, has spread to all world. Based on the accumulated data and knowledge on the coronavirus infection and immunology characteristics, this review would hope to give some hints on human immune response to SARS-CoV-2 infection in cancer patients. This insight may help in designing the appropriate immune intervention for treatment and the prophylactic/therapeutic methods against cancer under current coronavirus from immunopathology characteristics of SARS-CoV-2 and cancer entwisted with it. We should achieve accurate diagnosis and treatment for cancer patients through advantages of multidisciplinary diagnosis and treatment team. It is believed that we will eventually overcome the epidemic and win in the future.
    Keywords Medicine (General) ; R5-920
    Subject code 610
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher SAGE Publishing
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: 25(OH) D3 alleviate liver NK cytotoxicity in acute but not in chronic fibrosis model of BALB/c mice due to modulations in vitamin D receptor.

    Salhab, Ahmad / Amer, Johnny / Yinying, Lu / Safadi, Rifaat

    BMC gastroenterology

    2020  Volume 20, Issue 1, Page(s) 102

    Abstract: Background: Low 25-Hydroxy-vitamin-D; "25(OH)-D3" serum and vitamin D receptor (VDR) levels were recently correlated to advanced fibrosis. However, VDR mechanism in liver fibrosis modulations is not well understood. In this study, we aimed to evaluate ... ...

    Abstract Background: Low 25-Hydroxy-vitamin-D; "25(OH)-D3" serum and vitamin D receptor (VDR) levels were recently correlated to advanced fibrosis. However, VDR mechanism in liver fibrosis modulations is not well understood. In this study, we aimed to evaluate changes in liver NK cells cytotoxicity due to modulations in VDR in CCl
    Methods: Carbon-tetrachloride (CCl
    Results: Systemic inflammation and hepatic-fibrosis increased along 4 weeks of CCl
    Conclusion: Vitamin D alleviate liver NK cytotoxicity in acute but not in chronic fibrosis model due to modulations in vitamin D receptor and calcium. Hypercalcemia associated with late fibrosis may inhibited VDR levels, however, may not explain the profibrogenic effects of vitamin D.
    MeSH term(s) Acute Disease ; Animals ; Biomarkers/metabolism ; Calcifediol/metabolism ; Calcifediol/pharmacology ; Calcifediol/therapeutic use ; Calcium/metabolism ; Chronic Disease ; Killer Cells, Natural/drug effects ; Killer Cells, Natural/metabolism ; Liver/drug effects ; Liver/metabolism ; Liver/pathology ; Liver Cirrhosis/drug therapy ; Liver Cirrhosis/metabolism ; Liver Cirrhosis/pathology ; Male ; Mice ; Mice, Inbred BALB C ; Receptors, Calcitriol/metabolism ; Vitamins/metabolism ; Vitamins/pharmacology ; Vitamins/therapeutic use
    Chemical Substances Biomarkers ; Receptors, Calcitriol ; Vdr protein, mouse ; Vitamins ; Calcifediol (P6YZ13C99Q) ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2020-04-10
    Publishing country England
    Document type Evaluation Study ; Journal Article
    ISSN 1471-230X
    ISSN (online) 1471-230X
    DOI 10.1186/s12876-020-01248-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Analysis of TCR Repertoire by High-Throughput Sequencing Indicates the Feature of T Cell Immune Response after SARS-CoV-2 Infection

    Yifan Wang / Fugang Duan / Zhu Zhu / Meng Yu / Xiaodong Jia / Hui Dai / Pingzhang Wang / Xiaoyan Qiu / Yinying Lu / Jing Huang

    Cells, Vol 11, Iss 68, p

    2022  Volume 68

    Abstract: Coronavirus disease 2019 (COVID-19) is a global infectious disease caused by the SARS-CoV-2 coronavirus. T cells play an essential role in the body’s fighting against the virus invasion, and the T cell receptor (TCR) is crucial in T cell-mediated virus ... ...

    Abstract Coronavirus disease 2019 (COVID-19) is a global infectious disease caused by the SARS-CoV-2 coronavirus. T cells play an essential role in the body’s fighting against the virus invasion, and the T cell receptor (TCR) is crucial in T cell-mediated virus recognition and clearance. However, little has been known about the features of T cell response in convalescent COVID-19 patients. In this study, using 5′RACE technology and PacBio sequencing, we analyzed the TCR repertoire of COVID-19 patients after recovery for 2 weeks and 6 months compared with the healthy donors. The TCR clustering and CDR3 annotation were exploited to discover groups of patient-specific TCR clonotypes with potential SARS-CoV-2 antigen specificities. We first identified CD4 + and CD8 + T cell clones with certain clonal expansion after infection, and then observed the preferential recombination usage of V(D) J gene segments in CD4 + and CD8 + T cells of COVID-19 patients with different convalescent stages. More important, the TRBV6-5-TRBD2-TRBJ2-7 combination with high frequency was shared between CD4 + T and CD8 + T cells of different COVID-19 patients. Finally, we found the dominant characteristic motifs of the CDR3 sequence between recovered COVID-19 and healthy control. Our study provides novel insights on TCR in COVID-19 with different convalescent phases, contributing to our understanding of the immune response induced by SARS-CoV-2.
    Keywords SARS-CoV-2 ; COVID-19 ; T cell receptor ; CDR3 ; immune memory ; Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2022-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: A novel strategy for identifying biomarker in serum of patient with COVID-19 using immune complex

    Fugang Duan / Yifan Wang / Taoyu Chen / Zhu Zhu / Meng Yu / Hui Dai / Shangen Zheng / Yinying Lu / Tingting Li / Xiaoyan Qiu

    Signal Transduction and Targeted Therapy, Vol 7, Iss 1, Pp 1-

    2022  Volume 3

    Keywords Medicine ; R ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: The impact of receptor-binding domain natural mutations on antibody recognition of SARS-CoV-2

    Cheng Li / Xiaolong Tian / Xiaodong Jia / Jinkai Wan / Lu Lu / Shibo Jiang / Fei Lan / Yinying Lu / Yanling Wu / Tianlei Ying

    Signal Transduction and Targeted Therapy, Vol 6, Iss 1, Pp 1-

    2021  Volume 3

    Keywords Medicine ; R ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-03-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Oncolytic adenovirus programmed by synthetic gene circuit for cancer immunotherapy

    Huiya Huang / Yiqi Liu / Weixi Liao / Yubing Cao / Qiang Liu / Yakun Guo / Yinying Lu / Zhen Xie

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 15

    Abstract: It is difficult to improve the efficacy of oncolytic virotherapy due to immune system responses and limited understanding of population dynamics. Here the authors use synthetic biology gene circuits to control adenoviral replication and release of ... ...

    Abstract It is difficult to improve the efficacy of oncolytic virotherapy due to immune system responses and limited understanding of population dynamics. Here the authors use synthetic biology gene circuits to control adenoviral replication and release of immunomodulators in hepatocellular carcinoma cells.
    Keywords Science ; Q
    Language English
    Publishing date 2019-10-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Oncolytic adenovirus programmed by synthetic gene circuit for cancer immunotherapy

    Huiya Huang / Yiqi Liu / Weixi Liao / Yubing Cao / Qiang Liu / Yakun Guo / Yinying Lu / Zhen Xie

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 15

    Abstract: It is difficult to improve the efficacy of oncolytic virotherapy due to immune system responses and limited understanding of population dynamics. Here the authors use synthetic biology gene circuits to control adenoviral replication and release of ... ...

    Abstract It is difficult to improve the efficacy of oncolytic virotherapy due to immune system responses and limited understanding of population dynamics. Here the authors use synthetic biology gene circuits to control adenoviral replication and release of immunomodulators in hepatocellular carcinoma cells.
    Keywords Science ; Q
    Language English
    Publishing date 2019-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Preliminary exploration of survival analysis using the OHDSI common data model

    Na Hong / Ning Zhang / Huawei Wu / Shanshan Lu / Yue Yu / Li Hou / Yinying Lu / Hongfang Liu / Guoqian Jiang

    BMC Medical Informatics and Decision Making, Vol 18, Iss S5, Pp 81-

    a case study of intrahepatic cholangiocarcinoma

    2018  Volume 88

    Abstract: Abstract Background Data heterogeneity is a common phenomenon related to the secondary use of electronic health records (EHR) data from different sources. The Observational Health Data Sciences and Informatics (OHDSI) Common Data Model (CDM) organizes ... ...

    Abstract Abstract Background Data heterogeneity is a common phenomenon related to the secondary use of electronic health records (EHR) data from different sources. The Observational Health Data Sciences and Informatics (OHDSI) Common Data Model (CDM) organizes healthcare data into standard data structures using concepts that are explicitly and formally specified through standard vocabularies, thereby facilitating large-scale analysis. The objective of this study is to design, develop, and evaluate generic survival analysis routines built using the OHDSI CDM. Methods We used intrahepatic cholangiocarcinoma (ICC) patient data to implement CDM-based survival analysis methods. Our methods comprise the following modules: 1) Mapping local terms to standard OHDSI concepts. The analytical expression of variables and values related to demographic characteristics, medical history, smoking status, laboratory results, and tumor feature data. These data were mapped to standard OHDSI concepts through a manual analysis; 2) Loading patient data into the CDM using the concept mappings; 3) Developing an R interface that supports the portable survival analysis on top of OHDSI CDM, and comparing the CDM-based analysis results with those using traditional statistical analysis methods. Results Our dataset contained 346 patients diagnosed with ICC. The collected clinical data contains 115 variables, of which 75 variables were mapped to the OHDSI concepts. These concepts mainly belong to four domains: condition, observation, measurement, and procedure. The corresponding standard concepts are scattered in six vocabularies: ICD10CM, ICD10PCS, SNOMED, LOINC, NDFRT, and READ. We loaded a total of 25,950 patient data records into the OHDSI CDM database. However, 40 variables failed to map to the OHDSI CDM as they mostly belong to imaging data and pathological data. Conclusions Our study demonstrates that conducting survival analysis using the OHDSI CDM is feasible and can produce reusable analysis routines. However, challenges to be overcome include ...
    Keywords OHDSI CDM ; Survival analysis ; Multi-center analysis ; R ; Intrahepatic cholangiocarcinoma ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 310
    Language English
    Publishing date 2018-12-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: MiR-223 modulates hepatocellular carcinoma cell proliferation through promoting apoptosis via the Rab1-mediated mTOR activation

    Dong, Zheng / Ruizhao Qi / Xiaodong Guo / Xin Zhao / Yinyin Li / Zhen Zeng / Wenlin Bai / Xiujuan Chang / Liyan Hao / Yan Chen / Min Lou / Zhiwei Li / Yinying Lu

    Biochemical and biophysical research communications. 2017 Jan. 29, v. 483

    2017  

    Abstract: Hepatocellular carcinoma (HCC) is a common digestive malignancy. MiR-223, a well-identified miRNA, exhibits diverse properties in different cancers. In this study, we demonstrated that miR-223 could suppress cell growth and promote apoptosis in HepG2 and ...

    Abstract Hepatocellular carcinoma (HCC) is a common digestive malignancy. MiR-223, a well-identified miRNA, exhibits diverse properties in different cancers. In this study, we demonstrated that miR-223 could suppress cell growth and promote apoptosis in HepG2 and Bel-7402 HCC cell lines. We screened and identified a novel miR-223 target, Ras-related protein Rab-1(Rab1). Upregulation of miR-223 would specifically and markedly down-regulate Rab1 expression. In addition, miR-223-overexpressing subclones showed significant cell growth inhibition by increasing cell apoptosis in HepG2 and Bel-7402 cells. To identify the mechanisms, we firstly investigated the mTOR pathway and found that pmTOR, p70S6K and Bcl-2 were dramatically down-regulated after miR-223 transfection, while no changes in the level of Bax was visualized. Furthermore, our data showed that the anti-tumor effects arising from miR-223 transfection in HCC cells may be due to the deactivation of mTOR pathway caused by the suppression of Rab1 expression when miR-223 is overexpressed. In summary, our results indicate that miR-223 functions as a tumor suppressor and plays a critical role in inhibiting the tumorigenesis and promoting the apoptosis of HCC through the mTOR signaling pathway in vitro. By targeting Rab1, miR-223 efficiently mediates the mTOR pathway. Given these, miR-223 may be a potential therapeutic target for treating HCC.
    Keywords apoptosis ; carcinogenesis ; cell growth ; cell proliferation ; gene expression regulation ; gene overexpression ; growth retardation ; hepatoma ; microRNA ; neoplasm cells ; signal transduction ; transfection
    Language English
    Dates of publication 2017-0129
    Size p. 630-637.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 205723-2
    ISSN 0006-291X ; 0006-291X
    ISSN (online) 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2016.12.091
    Database NAL-Catalogue (AGRICOLA)

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