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  • PROJ Anaerobic hydrocarbon biodegradation by alkylotrophic methanogens in deep oil reservoirs

    Zhuo Zhou, Biogas Institute of Ministry of Agriculture and Rural Affairs,2023.02.22



  • PROJ Metagenomic sequencing for diagnosis of infectious and autoimmune encephalitis and meningitis

    Xiaozhou Pan, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University,2023.10.17


    In this study, we collected CSF samples from 152 pediatric patients from 2020 to 2022. By comparing the transcriptomic landscape of AE patients with that of IE patients including viral and bacterial infections, we found gene expression signatures specific to each type of encephalopathy. Finally, we identified markers of AE at the gene expression levels and validated in an additional cohort, thus highlighting the important value of mNGS in the clinical diagnosis of AE.


  • PROJ Global deep-sea sediment microbiomes

    Tianliang He, Zhejiang University,2024.02.19



  • PROJ Verstraetearchaea LWZ-6

    Kejia Wu, Biogas Institute of Ministry of Agriculture and Rural Affairs,2022.11.10


    A highly enriched microbial consortium from Shengli oil field sludge, containing a single archaeal species belonging to the phylum Verstraetearchaeota. The Verstraetearchaea LWZ-6 is a heterotrophic methanogen that utilizes methanol or monomethylamine as electron acceptors and hydrogen as electron donor.


  • PROJ PDK4-dependent hypercatabolism and lactate production of senescence cells promotes cancer malignancy

    Yu Sun, Shanghai Institute of Nutrition and Health, CAS,2023.12.28


    Technical advances in next generation sequencing (NGS) has revolutionized system-based analysis of genome-wide expression, cellular pathways and responses. We performed this study to establish the transcriptomic profiles of human prostate cancer cell lines exposed to conditioned media from human primary stromal cells engineered to express pyruvate dehydrogenase kinase 4 (PDK4), a key enzyme that is correlated with glucose metabolism, negatively regulates the conversion of pyruvate to acetyl-CoA and plays important roles in cancer progression and multiple other pathological events.


  • PROJ ARID2 mitigates hepatic steatosis via promoting the ubiquitination of JAK2 (house mouse)

    Jingjing Li, Shanghai Institute of Nutrition and Health, CAS,2023.12.27


    Non-alcoholic fatty liver disease (NAFLD) has become a growing public health problem. However, the complicated pathogenesis of NAFLD contributes to the deficiency of effective clinical treatment. Here, we elucidated that liver-specific loss of Arid2 induced hepatic steatosis and this progression could be exacerbated by HFD. Mechanistic study revealed that ARID2 repressed JAK2-STAT5-PPARγ signaling pathway by promoting the ubiquitination of JAK2, which was mediated by NEDD4L, a novel E3 ligase for JAK2. ChIP assay revealed that ARID2 recruited CARM1 to increase H3R17me2 level at NEDD4L promoter and activated the transcription of NEDD4L. Moreover, inhibition of Jak2 by Fedratinib in liver-specific Arid2 knockout mice alleviated HFD-induced hepatic steatosis. Downregulation of ARID2 and the reverse correlation between ARID2 and JAK2 were also observed in clinical samples. Therefore, our study has revealed an important role of ARID2 in the development of NAFLD and provides a potential therapeutic strategy for NAFLD. Overall design: Comparative gene expression profiling analysis of RNA-seq data for livers of Arid2 WT and LKO mice.


  • PROJ PPDPF suppresses the development of hepatocellular carcinoma through TRIM21-mediated ubiquitination of RIPK1

    Jingjing Li, Shanghai Institute of Nutrition and Health, CAS,2023.12.27


    Pancreatic progenitor cell differentiation and proliferation factor (PPDPF) has been reported to play a role in tumorigenesis. However, its function in hepatocellular carcinoma (HCC) remains poorly understood. In this study, we report that PPDPF is significantly downregulated in HCC and indicats poor prognosis and survival for HCC patients. In the DEN-induced HCC mouse model, hepatocyte-specific depletion of Ppdpf promots hepatocarcinogenesis, and reintroduction of PPDPF into LKO mice inhibits the accelerated HCC development. Mechanistic study reveals that PPDPF regulated NF-kB signaling through modulation of RIPK1 ubiquitination. PPDPF interacts with RIPK1 and facilitates K63-linked ubiquitination of RIPK1 via recruiting the E3 ligase TRIM21, which catalyzs K63-linked ubiquitination of RIPK1 on K140. In addition, liver-specific overexpression of PPDPF activats NF-kB signaling, attenuats apoptosis and compensatory proliferation in mice, which significantly suppresses HCC development. This work identifies PPDPF as a regulator of NF-kB signaling and provides a potential therapeutic candidate for HCC.


  • PROJ Transcriptomic profiling of senescent human stromal cells upon medicinal intervention with rutin (human)

    Yu Sun, Shanghai Institute of Nutrition and Health, CAS,2023.12.27


    Aging and age-related pathologies can be delayed by specifically targeting the senescence-associated secretory phenotype (SASP), a hallmark feature of senescent cells. Achieving the goal using natural or synthetic agents would have a tremendous impact on the quality of lifespan and burden of age-related chronic diseases. We report the potential of rutin, a bioactive phytochemical component derived from natural plants specifically ginkgo boliva, in targeting senescent cells via suppression of the SASP. This study demonstrates the efficacy of rutin as medicinal agent in controlling the influence of senescent human stromal cells and provides a strong rationale for its future use in aging intervention and geriatric medicine. Overall design: Examination of in vitro efficacy of rutin, a polyphenolic compound in treating human senescent stromal cells (PSC27 line). Ginkgo biloba products are widely consumed herbal supplements that contain ingredients with anti-oxidant potentials. However, the active agents in ginkgo biloba extracts (GBE) remain unclear, and its major ingredients such as rutin has not been extensively investigated in cellular senescence. This assay was performed beyond previous studies reporting the effects of GBE in anti-diabetic, anti-cataract therapy, anti-inflammation and anti-tumor therapies.


  • PROJ Targeting UHRF1-SAP30-MXD4 axis for leukemia initiating cell eradication in myeloid leukemia

    Wang lan, Shanghai Institute of Nutrition and Health,2023.12.11


    Aberrant self-renewal of leukemia initiation cells (LICs) drives aggressive acute myeloid leukemia (AML). Here, we report that UHRF1, an epigenetic regulator that recruits DNMT1 to methylate DNA, is highly expressed in AML and predicts poor prognosis. UHRF1 is required for myeloid leukemogenesis by maintaining self-renewal of LICs. Mechanistically, UHRF1 directly interacts with Sin3A associated protein 30 (SAP30) through two amino acids, G572 and F573 in its SRA domain, to repress gene expression. Depletion of UHRF1 or SAP30 derepresses an important target gene, MXD4, which encodes a MYC antagonist, and leads to suppression of leukemogenesis. Knockdown of MXD4 can rescue the leukemogenesis by activating the MYC pathway. Lastly, we identified a UHRF1 inhibitor, UF146, and demonstrated its significant therapeutic efficacy in the myeloid leukemia PDX model. Taken together, these studies reveal the mechanisms for altered epigenetic programs in AML and provide a promising targeted therapeutic strategy against AML.


  • PROJ Metatranscriptomic data in China Sea

    Jinxin Xu, Xiamen University,2023.03.12