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  1. Article: Pan-genome analysis of

    Zhou, You / Tu, Teng / Yao, Xueping / Luo, Yan / Yang, Zexiao / Ren, Meishen / Zhang, Ge / Yu, Yuanyuan / Lu, Aiping / Wang, Yin

    Frontiers in microbiology

    2024  Volume 15, Page(s) 1362316

    Abstract: Streptococcus ... ...

    Abstract Streptococcus suis
    Language English
    Publishing date 2024-02-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2024.1362316
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  2. Article: Pan-genome wide association study of

    Zhou, You / Jiang, Dike / Yao, Xueping / Luo, Yan / Yang, Zexiao / Ren, Meishen / Zhang, Ge / Yu, Yuanyuan / Lu, Aiping / Wang, Yin

    Frontiers in microbiology

    2023  Volume 14, Page(s) 1160433

    Abstract: Glaesserella ... ...

    Abstract Glaesserella parasuis
    Language English
    Publishing date 2023-04-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1160433
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  3. Article ; Online: Comprehensive analysis of REST corepressors (RCORs) in pan-cancer

    Rong Zheng / Yingying Pan / Xinhui Liu / Feiye Liu / Aimin Li / Dayong Zheng / Yue Luo

    Frontiers in Cell and Developmental Biology, Vol

    2023  Volume 11

    Abstract: ... of RCORs in pan-cancer. Clinical correlation, stemness index, immune infiltration and regulatory networks ... response, MSI, drug sensitivity and genetic alteration in pan-cancer. In HCC, RCORs were considered ... revealed the potential molecular mechanisms of RCORs in pan-cancer, offering a benchmark for disease ...

    Abstract REST corepressors (RCORs) are the core component of the LSD1/CoREST/HDACs transcriptional repressor complex, which have been revealed differently expressed in various cancers, but the therapeutic and prognostic mechanisms in cancer are still poorly understood. In this study, we analyzed expression, prognostic value, molecular subtypes, genetic alteration, immunotherapy response and drug sensitivity of RCORs in pan-cancer. Clinical correlation, stemness index, immune infiltration and regulatory networks of RCORs in hepatocellular carcinoma (HCC) were detected through TCGA and GSCA database. In-vitro experiments were conducted to explore the role of RCOR1 in HCC cells. The expression of RCORs varied among different cancers, and have prognostic values in several cancers. Cancer subtypes were categorized according to the expression of RCORs with clinical information. RCORs were significantly correlated with immunotherapy response, MSI, drug sensitivity and genetic alteration in pan-cancer. In HCC, RCORs were considered as potential predictor of stemness and also had association with immune infiltration. The ceRNA-TF-kinase regulatory networks of RCORs were constructed. Besides, RCOR1 acts as an oncogene in HCC and promotes the proliferation of HCC cells by inhibiting cell cycle arrest and cell apoptosis. Taken together, our study revealed the potential molecular mechanisms of RCORs in pan-cancer, offering a benchmark for disease-related research.
    Keywords RCORs ; pan-cancer ; prognosis ; biomarker ; HCC ; cell growth ; Biology (General) ; QH301-705.5
    Subject code 610
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Mechanisms and potential applications of COPS6 in pan-cancer therapy.

    Wu, Tong / Ji, Miao-Rong / Luo, Lian-Xiang

    World journal of clinical oncology

    2024  Volume 15, Issue 3, Page(s) 367–370

    Abstract: ... conducted a pan-cancer analysis using various bioinformatics techniques such as differential expression ...

    Abstract The COP9 signalosome subunit 6 (COPS6) is abnormally overexpressed in many malignancies, yet its precise role in carcinogenesis is unknown. To gain a better understanding of COPS6's role, the authors conducted a pan-cancer analysis using various bioinformatics techniques such as differential expression patterns, prognostic value, gene mutations, immune infiltration, correlation analysis, and functional enrichment assessment. Results showed that COPS6 was highly correlated with prognosis, immune cell infiltration level, tumor mutation burden, and microsatellite instability in patients with a range of tumor types. This suggests that COPS6 may be a potential target for cancer treatment. Overall, this research provides insight into COPS6's role in cancer development and its potential therapeutic applications.
    Language English
    Publishing date 2024-03-28
    Publishing country United States
    Document type Editorial
    ZDB-ID 2587357-X
    ISSN 2218-4333
    ISSN 2218-4333
    DOI 10.5306/wjco.v15.i3.367
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Pan-cancer analysis of ABCC1 as a potential prognostic and immunological biomarker.

    Wang, Tiantian / Rao, Dean / Fu, Chenan / Luo, Yiming / Lu, Junli / Liang, Huifang / Xia, Limin / Huang, Wenjie

    Translational oncology

    2024  Volume 41, Page(s) 101882

    Abstract: ... of various types of cancer. However, the impact of ABCC1 on cancer immune infiltration and pan-cancer ... prognosis has been rarely studied. Our comprehensive pan-cancer analysis unveiled elevated ABCC1 expression ...

    Abstract ABCC1 belongs to the ATP-binding cassette (ABC) superfamily, which encompasses a total of 48 constituent members. ABCC1 has been shown to be associated with the growth, progression, and drug resistance of various types of cancer. However, the impact of ABCC1 on cancer immune infiltration and pan-cancer prognosis has been rarely studied. Our comprehensive pan-cancer analysis unveiled elevated ABCC1 expression across various cancers. ABCC1 overexpression consistently predicted unfavorable outcomes based on TCGA data. Moreover, ABCC1 expression exhibited intricate associations with diverse immune-related genes and demonstrated a close correlation with immune scores across multiple tumor types. Analysis of scRNA-seq data from the GEO database revealed that the expression of ABCC1 in hepatocellular carcinoma (HCC) cells is significant positively correlated with macrophage infiltration. Furthermore, various in vitro and in vivo experiments substantiated the role of ABCC1 in promoting the progression of HCC, along with increased macrophage recruitment. Based on the results, we propose ABCC1 as a potentially valuable prognostic indicator and a prospective target for immune-based cancer therapies.
    Language English
    Publishing date 2024-01-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2443840-6
    ISSN 1936-5233
    ISSN 1936-5233
    DOI 10.1016/j.tranon.2024.101882
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  6. Article: Pan-Genomic Analysis Identifies the Chinese Strain as a New Subspecies of

    Wei, Feng / Liang, Xia / Shi, Jian-Cheng / Luo, Jing-Nan / Qiu, Li-Juan / Li, Xi-Xuan / Lu, Li-Juan / Wen, Ying-Qiang / Feng, Jia-Yue

    Plant disease

    2024  Volume 108, Issue 1, Page(s) 45–49

    Abstract: Xanthomonas ... ...

    Abstract Xanthomonas fragariae
    MeSH term(s) Genomics ; Multilocus Sequence Typing ; Xanthomonas/genetics
    Language English
    Publishing date 2024-01-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 754182-x
    ISSN 0191-2917
    ISSN 0191-2917
    DOI 10.1094/PDIS-05-23-0933-SC
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

    Z 2043: Show issues

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  7. Article ; Online: Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice.

    Zhong, Yuanyuan / Luo, Yuhong / Sun, Jinliang / Qin, Xuemei / Gan, Ping / Zhou, Zuwen / Qian, Yongqing / Zhao, Rupeng / Zhao, Zhiyuan / Cai, Wenguo / Luo, Jijing / Chen, Ling-Ling / Song, Jia-Ming

    The Plant cell

    2024  

    Abstract: ... cold tolerance. In this study, we constructed a rice pan-transcriptome and characterized its transcriptional ...

    Abstract Plants have evolved complex mechanisms to adapt to harsh environmental conditions. Rice (Oryza sativa) is a staple food crop that is sensitive to low temperatures. However, its cold stress responses remain poorly understood, thus limiting possibilities for crop engineering to achieve greater cold tolerance. In this study, we constructed a rice pan-transcriptome and characterized its transcriptional regulatory landscape in response to cold stress. We performed Iso-Seq and RNA-Seq of 11 rice cultivars subjected to a time-course cold treatment. Our analyses revealed that alternative splicing-regulated gene expression plays a significant role in the cold stress response. Moreover, we identified CATALASE C (OsCATC) and Os03g0701200 as candidate genes for engineering enhanced cold tolerance. Importantly, we uncovered central roles for the two serine-arginine-rich proteins OsRS33 and OsRS2Z38 in cold tolerance. Our analysis of cold tolerance and resequencing data from a diverse collection of 165 rice cultivars suggested that OsRS2Z38 may be a key selection gene in japonica domestication for cold adaptation, associated with the adaptive evolution of rice. This study systematically investigated the distribution, dynamic changes, and regulatory mechanisms of alternative splicing in rice under cold stress. Overall, our work generates a rich resource with broad implications for understanding the genetic basis of cold response mechanisms in plants.
    Language English
    Publishing date 2024-02-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 623171-8
    ISSN 1532-298X ; 1040-4651
    ISSN (online) 1532-298X
    ISSN 1040-4651
    DOI 10.1093/plcell/koae039
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    In stock of ZB MED Bonn / Germany

    Z 4952: Show issues

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  8. Article ; Online: Development and validation of a radiosensitivity model to evaluate radiotherapy benefits in pan-cancer.

    Yang, Qi / Zhou, Xinyi / Fang, Jianbo / Lin, Anqi / Zhang, Hongman / Cheng, Quan / Liu, Zaoqu / Luo, Peng / Zhang, Jian

    Cancer science

    2024  

    Abstract: ... in pan-cancer, we developed a model called Radiation Intrinsic Sensitivity Evaluation (RISE). The RISE ...

    Abstract Radiotherapy, one of the most fundamental cancer treatments, is confronted with the dilemma of treatment failure due to radioresistance. To predict the radiosensitivity and improve tumor treatment efficiency in pan-cancer, we developed a model called Radiation Intrinsic Sensitivity Evaluation (RISE). The RISE model was built using cell line-based mRNA sequencing data from five tumor types with varying radiation sensitivity. Through four cell-derived datasets, two public tissue-derived cohorts, and one local cohort of 42 nasopharyngeal carcinoma patients, we demonstrated that RISE could effectively predict the level of radiation sensitivity (area under the ROC curve [AUC] from 0.666 to 1 across different datasets). After the verification by the colony formation assay and flow cytometric analysis of apoptosis, our four well-established radioresistant cell models successfully proved higher RISE values in radioresistant cells by RT-qPCR experiments. We also explored the prognostic value of RISE in five independent TCGA cohorts consisting of 1137 patients who received radiation therapy and found that RISE was an independent adverse prognostic factor (pooled multivariate Cox regression hazard ratio [HR]: 1.84, 95% CI 1.39-2.42; p < 0.01). RISE showed a promising ability to evaluate the radiotherapy benefit while predicting the prognosis of cancer patients, enabling clinicians to make individualized radiotherapy strategies in the future and improve the success rate of radiotherapy.
    Language English
    Publishing date 2024-04-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2115647-5
    ISSN 1349-7006 ; 1349-7006
    ISSN (online) 1349-7006
    ISSN 1349-7006
    DOI 10.1111/cas.16168
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Multiomics characteristics and immunotherapeutic potential of EZH2 in pan-cancer.

    Luo, Lianghua / Wang, Zhonghao / Hu, Tengcheng / Feng, Zongfeng / Zeng, Qingwen / Shu, Xufeng / Wu, Ahao / Huang, Pan / Cao, Yi / Tu, Yi / Li, Zhengrong

    Bioscience reports

    2022  Volume 43, Issue 1

    Abstract: ... in pan-cancer remain unclear. Transcriptome and clinical raw data of pan-cancer samples were acquired ... from pan-cancer insight. Finally, quantitative reverse transcription polymerase chain reaction and ...

    Abstract Enhancer of zeste homolog 2 (EZH2) is a significant epigenetic regulator that plays a critical role in the development and progression of cancer. However, the multiomics features and immunological effects of EZH2 in pan-cancer remain unclear. Transcriptome and clinical raw data of pan-cancer samples were acquired from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and subsequent data analyses were conducted by using R software (version 4.1.0). Furthermore, numerous bioinformatics analysis databases also reapplied to comprehensively explore and elucidate the oncogenic mechanism and therapeutic potential of EZH2 from pan-cancer insight. Finally, quantitative reverse transcription polymerase chain reaction and immunohistochemical assays were performed to verify the differential expression of EZH2 gene in various cancers at the mRNA and protein levels. EZH2 was widely expressed in multiple normal and tumor tissues, predominantly located in the nucleoplasm. Compared with matched normal tissues, EZH2 was aberrantly expressed in most cancers either at the mRNA or protein level, which might be caused by genetic mutations, DNA methylation, and protein phosphorylation. Additionally, EZH2 expression was correlated with clinical prognosis, and its up-regulation usually indicated poor survival outcomes in cancer patients. Subsequent analysis revealed that EZH2 could promote tumor immune evasion through T-cell dysfunction and T-cell exclusion. Furthermore, expression of EZH2 exhibited a strong correlation with several immunotherapy-associated responses (i.e., immune checkpoint molecules, tumor mutation burden (TMB), microsatellite instability (MSI), mismatch repair (MMR) status, and neoantigens), suggesting that EZH2 appeared to be a novel target for evaluating the therapeutic efficacy of immunotherapy.
    MeSH term(s) Humans ; Multiomics ; Enhancer of Zeste Homolog 2 Protein/genetics ; Neoplasms/genetics ; Neoplasms/therapy ; Computational Biology ; Immunotherapy
    Chemical Substances Enhancer of Zeste Homolog 2 Protein (EC 2.1.1.43) ; EZH2 protein, human (EC 2.1.1.43)
    Language English
    Publishing date 2022-12-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 764946-0
    ISSN 1573-4935 ; 0144-8463
    ISSN (online) 1573-4935
    ISSN 0144-8463
    DOI 10.1042/BSR20222230
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1676: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  10. Article: Pan-cancer analysis revealed prognosis value and immunological relevance of RAMPs.

    Yang, Sha / Huan, Renzheng / Deng, Mei / Luo, Tao / Peng, Shuo / Xiong, Yunbiao / Han, Guoqiang / Liu, Jian / Zhang, Jiqin / Tan, Ying

    Heliyon

    2024  Volume 10, Issue 3, Page(s) e24849

    Abstract: Whether receptor activity-modifying proteins (RAMPs) play a key role in human cancer prognosis and immunity remains unknown. We used data from the public databases, The Cancer Genome Atlas, Therapeutically Applicable Research to Generate Effective ... ...

    Abstract Whether receptor activity-modifying proteins (RAMPs) play a key role in human cancer prognosis and immunity remains unknown. We used data from the public databases, The Cancer Genome Atlas, Therapeutically Applicable Research to Generate Effective Treatments, and the Genotype-Tissue Expression project. We utilized bioinformatics methods, R software, and a variety of online databases to analyze RAMPs. In general, RAMPs were significantly and differentially expressed in multiple tumors, and RAMP expression was closely associated with prognosis, immune checkpoints, RNA-editing genes, tumor mutational burden, microsatellite instability, ploidy, and stemness indices. In addition, the expression of RAMPs is strongly correlated with tumor-infiltrating lymphocytes in human cancers. Moreover, the RAMP co-expression network is largely involved in many immune-related biological processes. Quantitative reverse transcription polymerase chain reaction and Western blot proved that RAMP3 was highly expressed in glioma, and RAMP3 promoted tumor proliferation and migration. RAMPs exhibit potential as prognostic and immune-related biomarkers in human cancers. Moreover, RAMPs can be potentially developed as therapeutic targets or used to enhance the efficacy of immunotherapy.
    Language English
    Publishing date 2024-01-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2024.e24849
    Database MEDical Literature Analysis and Retrieval System OnLINE

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