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  • PROJ Molecular Landscape and Subtype-Specific Therapeutic Response of Nasopharyngeal Carcinoma Revealed by Integrative Pharmacogenomics for Precision Oncology

    Lyu Xueying, University of Macau,2021.01.26


    Nasopharyngeal carcinoma (NPC) is a malignant head and neck cancer with high morbidity in Southeast Asia, however the pathogenic mechanism of this disease is poorly understood. Using integrative pharmacogenomics, we found that NPC subtypes maintained distinct molecular features, drug responsiveness, and graded radiation sensitivity. The epithelial carcinoma (EC) subtype was characterized by activations of microtubule polymerization and defective mitotic spindle checkpoint related genes, while sarcomatoid carcinoma (SC) and mixed sarcomatoid-epithelial carcinoma (MSEC) subtypes exhibited enriched epithelial-mesenchymal transition and invasion promoting genes, which was well correlated with their morphological features. Furthermore, patient-derived organoid (PDO) based drug test identified potential subtype-specific treatment regimens in that SC and MSEC subtypes were sensitive to microtubule inhibitors, whereas EC subtype was more responsive to EGFR inhibitors, which was synergistically enhanced by combining with radiotherapy. Through combinational chemoradiotherapy (CRT) screening, effective CRT regimens were also suggested for patients showing less sensitivity to radiation. Altogether, our study provided the first example of applying integrative pharmacogenomics to establish a personalized precision oncology for NPC subtype-guided therapies.


  • PROJ Spatial and single-cell transcriptomics landscape of adenomyosis

    Guihua Liu, The Sixth Affiliated Hospital of Sun Yat-sen University,2023.05.26


    Adenomyosis is a prevalent and non-cancerous uterine disease which can significantly impaired the fertility of reproductive-age women. However, the etiology, as well as the cellular and molecular mechanism underlying adenomyosis remain largely unknown. Here, we utilized cutting-edge spatial and single-cell RNA sequencing technologies to create a comprehensive transcriptional atlas of adenomyosis pathology. Our spatial profiling clearly distinguished gland, mesenchyma and myometrium regions, recapitulating spatial transcriptome structural characteristics of uterus. Moreover, we analyzed the expression profiles of 69,115 single cells and integrated them with spatial data. The analysis of immune cells showed a distinct immune inflammatory microenvironment in the eutopic and ectopic endometrial glands of adenomyosis. Notably, we discovered an increased number of DNAH9+ ciliated cells in ectopic endometrial glands, indicating their potential role in the formation of ectopic endometrium. These findings provide cellular evidence to support the invagination theory and offer a new vision on the pathophysiology and clinical intervention of adenomyosis.


  • PROJ Deciphering key regulators involved in development of Hepatocellular carcinoma through whole transcriptome and proteome analysis

    Fang Xu, Zhengzhou University,2021.01.16


    The proteomics and transcriptomics of HCC were studied by TMT labeled tandem mass spectrometry and RNA sequencing respectively. The mRNA, miRNA, lncRNA and circRNA in HCC tumor and adjacent normal tissues were sequenced.A total of 977 proteins and 234 genes were profiled differently expressed in HCC tumor compared with adjacent normal tissues. Combined with the results above, 56 differently expressed proteins and genes (DEP-DEGs) with common changes in relative quantity were identified, including UDP-glucuronosyltransferase (UGT) and Cytochrome P450(CYP). Functional pathway analysis showed that the DEP-DEGs were mainly enriched in spliceosome and various metabolic processes.


  • PROJ Single-cell Atlas of Human IVD

    Jian He, Army Medical University,2022.05.10


    Single-cell sequencing of cells from 2 human healthy nucleus pulposus in IVD using the 10X genomics Kit.


  • PROJ FUSCC BRCA sequencing data

    Hongxia Zhou, Fudan University Shanghai Cancer Center,2023.10.20


    Significant strides in the realm of next-generation sequencing technology have facilitated its widespread adoption as a clinical tool. In this study, we executed an extensive prospective clinical sequencing initiative employing the Fudan-BC panel, and conducted a comprehensive examination of both the clinical and genomic attributes of Chinese breast cancer patients. Over the period spanning from April 1, 2018, to July 1, 2021, a total of 4405 consecutive patients of Chinese descent who received treatment at the Department of Breast Surgery at Fudan University Shanghai Cancer Center (FUSCC) were included in this cohort. In addition, we also included several patients receiving immunotherapy, PARP inhibitors, and CDK4/6 inhibitors in this cohort.


  • PROJ FUSCC PCMC mutation data

    Yuchen Pei, Fudan University Shanghai Cancer Center,2022.06.22


    Remarkable advances in next-generation sequencing technology enable the wide usage of sequencing as a clinical tool. Here, we conducted a large-scale prospective clinical sequencing program using the Fudan-BC panel, and comprehensively analyzed the clinical and genomic characteristics for Chinese breast cancer. A total of 4,079 consecutive Chinese patients who were treated at the Department of Breast Surgery at Fudan University Shanghai Cancer Center (FUSCC) were enrolled in this cohort from April 1, 2018, to June 1, 2021.


  • PROJ Microbiome of Li Shu soils

    yangfeng hu, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences,2023.10.23


    The main obiective of this project is to assess the changes in soil physical, chemical, functional, andbiological properties due to the land use change from conventional tillage to 'Lishu model' of conservation tillage.


  • PROJ Pharmaco-proteogenomics characterization of liver cancer organoids for precision oncology

    Yidi Sun, Shanghai Institutes for Biological Sciences,2022.03.07



  • PROJ The E3 ubiquitin ligase MARCH2 protects against myocardial ischemia-reperfusion injury

    liu shuolin, ,2023.09.25


    Inflammasome activation and pyroptotic cell death are known to contribute to the pathogenesis of cardiovascular diseases, such as myocardial ischemia-reperfusion (I/R) injury, although the underlying regulatory mechanisms remain poorly understood. Here we report that loss of E3 ubiquitin ligase membrane-associated RING finger protein 2 (MARCH2) prompted activation of NLRP3 inflammasome in cardiomyocytes.


  • PROJ test step by step multipel project

    node_dev node_dev, Shanghai Institute of Nutrition ang Health, CAS-MPG Partner Institute for Computational Biology,2020.02.28


    consequences of such alterations are mostly undefined. Here we report that the Hippo-YAP signaling, a key pathway that regulates cell proliferation and organ size, is under control of a new splicing switch. We show that