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  1. Article: Importance score of SARS-CoV-2 genome predicts the death risk of COVID-19.

    Cui, Chunmei / Cui, Qinghua

    Cell death discovery

    2022  Volume 8, Issue 1, Page(s) 303

    Language English
    Publishing date 2022-07-02
    Publishing country United States
    Document type Letter
    ISSN 2058-7716
    ISSN 2058-7716
    DOI 10.1038/s41420-022-01100-7
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  2. Article: Anti-

    Yan, Weifeng / Cui, Zhe / Li, Wenxin / An, Xin / Cheng, Xu / Wang, Sihong / Jin, Chunmei

    Die Pharmazie

    2024  Volume 78, Issue 11, Page(s) 225–230

    Abstract: New anti- ...

    Abstract New anti-
    MeSH term(s) Animals ; Mice ; Saponins/pharmacology ; Toxoplasma ; Panax ; Polysaccharides/pharmacology
    Chemical Substances Saponins ; Polysaccharides
    Language English
    Publishing date 2024-01-05
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 208793-5
    ISSN 0031-7144
    ISSN 0031-7144
    DOI 10.1691/ph.2023.3622
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Identification and Analysis of Sex-Biased MicroRNAs in Human Diseases.

    Zhong, Bitao / Cui, Chunmei / Cui, Qinghua

    Genes

    2023  Volume 14, Issue 9

    Abstract: It is well known that significant differences exist between males and females in both physiology and disease. Thus, it is important to identify and analyze sex-biased miRNAs. However, previous studies investigating sex differences in miRNA expression ... ...

    Abstract It is well known that significant differences exist between males and females in both physiology and disease. Thus, it is important to identify and analyze sex-biased miRNAs. However, previous studies investigating sex differences in miRNA expression have predominantly focused on healthy individuals or restricted their analysis to a single disease. Therefore, it is necessary to comprehensively identify and analyze the sex-biased miRNAs in diseases. For this purpose, in this study, we first identified the miRNAs showing sex-biased expression between males and females in diseases based on a number of miRNA expression datasets. Then, we performed a bioinformatics analysis for these sex-biased miRNAs. Notably, our findings revealed that women exhibit a greater number of conserved miRNAs that are highly expressed compared to men, and these miRNAs are implicated in a broader spectrum of diseases. Additionally, we explored the enriched transcription factors, functions, and diseases associated with these sex-biased miRNAs using the miRNA set enrichment analysis tool TAM 2.0. The insights gained from this study could carry implications for endeavors such as precision medicine and possibly pave the way for more targeted and tailored approaches to disease management.
    Language English
    Publishing date 2023-08-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14091688
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Combating pancreatic cancer with ovarian cancer cells.

    Lin, Xiao / Cui, Chunmei / Cui, Qinghua

    Aging

    2023  Volume 15, Issue 6, Page(s) 2189–2207

    Abstract: With overall five-year survival rate less than 10%, pancreatic cancer (PC) represents the most lethal one in all human cancers. Given that the incidence of PC is still increasing and current cancer treatment strategies are often inefficacious, its ... ...

    Abstract With overall five-year survival rate less than 10%, pancreatic cancer (PC) represents the most lethal one in all human cancers. Given that the incidence of PC is still increasing and current cancer treatment strategies are often inefficacious, its therapy is still a huge challenge. Here, we first revealed ovarian serous carcinoma is mostly anti-correlated with pancreatic cancer in gene expression signatures. Based on this observation, we proposed that ovarian cancer cells could defend PC. To confirm this strategy, we first showed that ovarian cancer cell SKOV3 can significantly inhibit the proliferation of pancreatic cancer cell SW1990 when they were co-cultured. We further validated this strategy by an animal model of pancreatic cancer xenografts. The result showed that the injection of SKOV3 significantly inhibits pancreatic cancer xenografts. Moreover, we found that SKOV3 with transgenic African elephant
    MeSH term(s) Animals ; Humans ; Female ; Ovarian Neoplasms/pathology ; Pancreatic Neoplasms/pathology ; Carcinoma, Ovarian Epithelial ; Cell Proliferation ; Cell Line, Tumor ; Apoptosis ; Pancreatic Neoplasms
    Language English
    Publishing date 2023-03-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1945-4589
    ISSN (online) 1945-4589
    DOI 10.18632/aging.204608
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: HMDD v4.0: a database for experimentally supported human microRNA-disease associations.

    Cui, Chunmei / Zhong, Bitao / Fan, Rui / Cui, Qinghua

    Nucleic acids research

    2023  Volume 52, Issue D1, Page(s) D1327–D1332

    Abstract: MicroRNAs (miRNAs) are a class of important small non-coding RNAs with critical molecular functions in almost all biological processes, and thus, they play important roles in disease diagnosis and therapy. Human MicroRNA Disease Database (HMDD) ... ...

    Abstract MicroRNAs (miRNAs) are a class of important small non-coding RNAs with critical molecular functions in almost all biological processes, and thus, they play important roles in disease diagnosis and therapy. Human MicroRNA Disease Database (HMDD) represents an important and comprehensive resource for biomedical researchers in miRNA-related medicine. Here, we introduce HMDD v4.0, which curates 53530 miRNA-disease association entries from literatures. In comparison to HMDD v3.0 released five years ago, HMDD v4.0 contains 1.5 times more entries. In addition, some new categories have been curated, including exosomal miRNAs implicated in diseases, virus-encoded miRNAs involved in human diseases, and entries containing miRNA-circRNA interactions. We also curated sex-biased miRNAs in diseases. Furthermore, in a case study, disease similarity analysis successfully revealed that sex-biased miRNAs related to developmental anomalies are associated with a number of human diseases with sex bias. HMDD can be freely visited at http://www.cuilab.cn/hmdd.
    MeSH term(s) Humans ; Databases, Nucleic Acid ; MicroRNAs/genetics ; Disease/genetics
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2023-08-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad717
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1067: Show issues Location:
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  6. Article ; Online: G Protein-Coupled Receptor 40 Agonist LY2922470 Alleviates Ischemic-Stroke-Induced Acute Brain Injury and Functional Alterations in Mice.

    Lu, Yingyu / Zhou, Wanlu / Cui, Qinghua / Cui, Chunmei

    International journal of molecular sciences

    2023  Volume 24, Issue 15

    Abstract: Stroke is a major cause of fatalities and disabilities around the world, yet the available treatments for it are still limited. The quest for more efficacious drugs and therapies is still an arduous task. LY2922470 is currently used as a G protein- ... ...

    Abstract Stroke is a major cause of fatalities and disabilities around the world, yet the available treatments for it are still limited. The quest for more efficacious drugs and therapies is still an arduous task. LY2922470 is currently used as a G protein-coupled receptor 40 (GPR40) agonist for the treatment of type 2 diabetes. Previous studies have reported protective effects of other GPR40 activators on the brain; however, it remains unclear whether LY2922470 could be a new stroke therapy and improve the stroke-induced brain damage. Here, we first reveal that the transcriptomic gene signature induced by LY2922470 is highly similar to those induced by some agents being involved in defending from cerebrovascular accidents and transient ischemic attacks, including acetylsalicylic acid, progesterone, estradiol, dipyridamole, and dihydroergotamine. This result thus suggests that LY2922470 could have protective effects against ischemic stroke. As a result, further experiments show that giving the small molecule LY2922470 via oral administration or intraperitoneal injection was seen to have a positive effect on neuroprotection with a reduction in infarct size and an improvement in motor skills in mice. Finally, it was demonstrated that LY2922470 could successfully mitigate the harm to the brain caused by ischemic stroke.
    MeSH term(s) Mice ; Animals ; Diabetes Mellitus, Type 2 ; Stroke/drug therapy ; Stroke/prevention & control ; Brain Ischemia/drug therapy ; Ischemic Stroke ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/agonists ; Brain Injuries ; Mice, Inbred C57BL
    Chemical Substances LY2922470 ; Receptors, G-Protein-Coupled
    Language English
    Publishing date 2023-07-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms241512244
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: G Protein-Coupled Receptor 40 Agonist LY2922470 Alleviates Ischemic-Stroke-Induced Acute Brain Injury and Functional Alterations in Mice

    Yingyu Lu / Wanlu Zhou / Qinghua Cui / Chunmei Cui

    International Journal of Molecular Sciences, Vol 24, Iss 12244, p

    2023  Volume 12244

    Abstract: Stroke is a major cause of fatalities and disabilities around the world, yet the available treatments for it are still limited. The quest for more efficacious drugs and therapies is still an arduous task. LY2922470 is currently used as a G protein- ... ...

    Abstract Stroke is a major cause of fatalities and disabilities around the world, yet the available treatments for it are still limited. The quest for more efficacious drugs and therapies is still an arduous task. LY2922470 is currently used as a G protein-coupled receptor 40 (GPR40) agonist for the treatment of type 2 diabetes. Previous studies have reported protective effects of other GPR40 activators on the brain; however, it remains unclear whether LY2922470 could be a new stroke therapy and improve the stroke-induced brain damage. Here, we first reveal that the transcriptomic gene signature induced by LY2922470 is highly similar to those induced by some agents being involved in defending from cerebrovascular accidents and transient ischemic attacks, including acetylsalicylic acid, progesterone, estradiol, dipyridamole, and dihydroergotamine. This result thus suggests that LY2922470 could have protective effects against ischemic stroke. As a result, further experiments show that giving the small molecule LY2922470 via oral administration or intraperitoneal injection was seen to have a positive effect on neuroprotection with a reduction in infarct size and an improvement in motor skills in mice. Finally, it was demonstrated that LY2922470 could successfully mitigate the harm to the brain caused by ischemic stroke.
    Keywords stroke ; LY2922470 ; ischemic stroke ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 616
    Language English
    Publishing date 2023-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: The role of CEMIP in cancers and its transcriptional and post-transcriptional regulation.

    Guo, Song / Guo, Yunfei / Chen, Yuanyuan / Cui, Shuaishuai / Zhang, Chunmei / Chen, Dahu

    PeerJ

    2024  Volume 12, Page(s) e16930

    Abstract: CEMIP is a protein known for inducing cell migration and binding to hyaluronic acid. Functioning as a hyaluronidase, CEMIP primarily facilitates the breakdown of the extracellular matrix component, hyaluronic acid, thereby regulating various signaling ... ...

    Abstract CEMIP is a protein known for inducing cell migration and binding to hyaluronic acid. Functioning as a hyaluronidase, CEMIP primarily facilitates the breakdown of the extracellular matrix component, hyaluronic acid, thereby regulating various signaling pathways. Recent evidence has highlighted the significant role of CEMIP in different cancers, associating it with diverse pathological states. While identified as a biomarker for several diseases, CEMIP's mechanism in cancer seems distinct. Accumulating data suggests that CEMIP expression is triggered by chemical modifications to itself and other influencing factors. Transcriptionally, chemical alterations to the CEMIP promoter and involvement of transcription factors such as AP-1, HIF, and NF-κB regulate CEMIP levels. Similarly, specific miRNAs have been found to post-transcriptionally regulate CEMIP. This review provides a comprehensive summary of CEMIP's role in various cancers and explores how both transcriptional and post-transcriptional mechanisms control its expression.
    MeSH term(s) Hyaluronic Acid/metabolism ; Cell Line, Tumor ; Hyaluronoglucosaminidase/genetics ; Gene Expression Regulation ; MicroRNAs/genetics ; Neoplasms/genetics
    Chemical Substances Hyaluronic Acid (9004-61-9) ; Hyaluronoglucosaminidase (EC 3.2.1.35) ; MicroRNAs
    Language English
    Publishing date 2024-02-19
    Publishing country United States
    Document type Review ; Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359 ; 2167-8359
    ISSN (online) 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.16930
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: A fusion framework of deep learning and machine learning for predicting sgRNA cleavage efficiency.

    Liu, Yu / Fan, Rui / Yi, Jingkun / Cui, Qinghua / Cui, Chunmei

    Computers in biology and medicine

    2023  Volume 165, Page(s) 107476

    Abstract: CRISPR/Cas9 system is a powerful tool for genome editing. Numerous studies have shown that sgRNAs can strongly affect the efficiency of editing. However, it is still not clear what rules should be followed for designing sgRNA with high cleavage ... ...

    Abstract CRISPR/Cas9 system is a powerful tool for genome editing. Numerous studies have shown that sgRNAs can strongly affect the efficiency of editing. However, it is still not clear what rules should be followed for designing sgRNA with high cleavage efficiency. At present, several machine learning or deep learning methods have been developed to predict the cleavage efficiency of sgRNAs, however, the prediction accuracy of these tools is still not satisfactory. Here we propose a fusion framework of deep learning and machine learning, which first deals with the primary sequence and secondary structure features of the sgRNAs using both convolutional neural network (CNN) and recurrent neural network (RNN), and then uses the features extracted by the deep neural network to train a conventional machine learning model with LGBM. As a result, the new approach overwhelmed previous methods. The Spearman's correlation coefficient between predicted and measured sgRNA cleavage efficiency of our model (0.917) is improved by over 5% compared with the most advanced method (0.865), and the mean square error reduces from 7.89 × 10
    MeSH term(s) Deep Learning ; RNA, Guide, CRISPR-Cas Systems ; Machine Learning ; Neural Networks, Computer
    Chemical Substances RNA, Guide, CRISPR-Cas Systems
    Language English
    Publishing date 2023-09-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2023.107476
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Defining the single base importance of human mRNAs and lncRNAs.

    Fan, Rui / Ji, Xiangwen / Li, Jianwei / Cui, Qinghua / Cui, Chunmei

    Briefings in bioinformatics

    2023  Volume 24, Issue 5

    Abstract: As the fundamental unit of a gene and its transcripts, nucleotides have enormous impacts on the gene function and evolution, and thus on phenotypes and diseases. In order to identify the key nucleotides of one specific gene, it is quite crucial to ... ...

    Abstract As the fundamental unit of a gene and its transcripts, nucleotides have enormous impacts on the gene function and evolution, and thus on phenotypes and diseases. In order to identify the key nucleotides of one specific gene, it is quite crucial to quantitatively measure the importance of each base on the gene. However, there are still no sequence-based methods of doing that. Here, we proposed Base Importance Calculator (BIC), an algorithm to calculate the importance score of each single base based on sequence information of human mRNAs and long noncoding RNAs (lncRNAs). We then confirmed its power by applying BIC to three different tasks. Firstly, we revealed that BIC can effectively evaluate the pathogenicity of both genes and single bases through single nucleotide variations. Moreover, the BIC score in The Cancer Genome Atlas somatic mutations is able to predict the prognosis of some cancers. Finally, we show that BIC can also precisely predict the transmissibility of SARS-CoV-2. The above results indicate that BIC is a useful tool for evaluating the single base importance of human mRNAs and lncRNAs.
    MeSH term(s) Humans ; COVID-19/genetics ; RNA, Long Noncoding/genetics ; SARS-CoV-2/genetics ; Algorithms ; Nucleotides ; RNA, Messenger/genetics
    Chemical Substances RNA, Long Noncoding ; Nucleotides ; RNA, Messenger
    Language English
    Publishing date 2023-09-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbad321
    Database MEDical Literature Analysis and Retrieval System OnLINE

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