INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
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2022
·Vol. 23
·期 7
·3833
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IF 6.208
Mengling Huang,Abrar Ahmed,Wei Wang,Xue Wang,Cui Ma,Haowei Jiang,Wei Li,Lili Jing
Gene expression is tightly regulated during hematopoiesis. Recent studies have suggested that RNA polymerase II (Pol II) promoter proximal pausing, a temporary stalling downstream of the promoter region after initiation, plays a critical role in regulating the expression of various genes in metazoans. However, the function of proximal pausing in hematopoietic gene regulation remains largely unknown. The negative elongation factor (NELF) complex is a key factor important for this proximal pausing. Previous studies have suggested that NELF regulates granulocytic differentiation in vitro, but its in vivo function during hematopoiesis remains uncharacterized. Here, we generated the zebrafish mutant for one NELF complex subunit Nelfb using the CRISPR-Cas9 technology. We found that the loss ofnelfbselectively induced excessive granulocytic development during primitive and definitive hematopoiesis. The loss ofnelfbreduced hematopoietic progenitor cell formation and did not affect erythroid development. Moreover, the accelerated granulocytic differentiation and reduced progenitor cell development could be reversed by inhibiting Pol II elongation. Further experiments demonstrated that the other NELF complex subunits (Nelfa and Nelfe) played similar roles in controlling granulocytic development. Together, our studies suggested that NELF is critical in controlling the proper granulocytic development in vivo, and that promoter proximal pausing might help maintain the undifferentiated state of hematopoietic progenitor cells.Keywords:zebrafish;negative elongation factor;RNA polymerase II promoter proximal pausing;granulocytic development
研究领域:
分子生物学
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血液学
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发育生物学
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遗传学
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DOI
PubMed
高影响因子
ADVANCED MATERIALS
·
2024
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IF 27.4
Manyu Chen,Yan Lu,Yuhan Liu,Quanying Liu,Siyan Deng,Yuan Liu,Xiaolin Cui,Jie Liang,Xingdong Zhang,Yujiang Fan,Qiguang Wang
Abnormal silencing of fibroblast growth factor (FGF) signaling significantly contributes to joint dysplasia and osteoarthritis (OA); However, the clinical translation of FGF18-based protein drugs is hindered by their short half-life, low delivery efficiency and the need for repeated articular injections. This study proposes a CRISPR/Cas9-based approach to effectively activate the FGF18 gene of OA chondrocytes at the genome level in vivo, using chondrocyte-affinity peptide (CAP) incorporated hybrid exosomes (CAP/FGF18-hyEXO) loaded with an FGF18-targeted gene-editing tool. Furthermore, CAP/FGF18-hyEXO are encapsulated in methacrylic anhydride-modified hyaluronic (HAMA) hydrogel microspheres via microfluidics and photopolymerization to create an injectable microgel system (CAP/FGF18-hyEXO@HMs) with self-renewable hydration layers to provide persistent lubrication in response to frictional wear. Together, the injectable CAP/FGF18-hyEXO@HMs, combined with in vivo FGF18 gene editing and continuous lubrication, have demonstrated their capacity to synergistically promote cartilage regeneration, decrease inflammation, and prevent ECM degradation both in vitro and in vivo, holding great potential for clinical translation.
研究领域:
生物医学工程
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基因治疗
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骨科
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再生医学
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DOI
PubMed
高影响因子
Advanced Science
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2024
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IF 14.3
Weina Fan,Jian Huang,Fanglin Tian,Xin Hong,Kexin Zhu,Yuning Zhan,Xin Li,Xiangyu Wang,Xin Wang,Li Cai,Ying Xing
Alternative splicing (AS) generates protein diversity and is exploited by cancer cells to drive tumor progression and resistance to many cancer therapies, including chemotherapy. SNRPA is first identified as a spliceosome-related gene that potentially modulates resistance to platinum chemotherapy. Both the knockout or the knockdown of SNRPA via CRISPR/Cas9 and shRNA techniques can reverse the resistance of cisplatin-resistant lung adenocarcinoma (LUAD) cells to cisplatin. SNRPA overexpression enhanced the resistance of cisplatin-sensitive LUAD cells. Gene Ontology (GO) analysis reveals that SNRPA is associated with DNA damage repair. Depletion of SNRPA induced ERCC1 exon 8 skipping and reduced ERCC1–XPF complex formation, whereas SNRPA overexpression exerted the opposite effect. siRNAs targeting isoforms containing ERCC1 exon 8 [ERCC1-E8 (+)] reversed SNRPA-enhanced cisplatin resistance and DNA damage repair. Furthermore, the IGF2BP protein, an m 6 A reader, and the ELAVL1 protein, an RNA stabilizer recruited by IGF2BP1, are found to bind to the SNRPA mRNA. ELAVL1 promoted cisplatin resistance, DNA repair and ERCC1-E8 (+) expression in an SNRPA-dependent manner. In a mouse xenograft model, SNRPA- KO CRISPR enhanced the sensitivity of LUAD cells to cisplatin. Overall, this study illuminates the role of SNRPA in platinum-based drug resistance, thereby providing a novel avenue to potentially enhance chemosensitivity and improve the prognosis of patients with LUAD.
研究领域:
癌症生物学
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分子生物学
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遗传学
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药理学
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肿瘤学
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产品关联
DOI
PubMed
高影响因子
Nature Communications
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2023
·Vol. 14
·期 1
·1-10
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IF 16.6
Yue Qun,Meng Jie,Qiu Yue,Yin Miaomiao,Zhang Liwen,Zhou Weiping,An Zhiqiang,Liu Zihe,Yuan Qipeng,Sun Wentao,Li Chun,Zhao Huimin,Molnár István,Xu Yuquan,Shi Shuobo
Synthetic biology requires efficient systems that support the well-coordinated co-expression of multiple genes. Here, we discover a 9-bp nucleotide sequence that enables efficient polycistronic gene expression in yeasts and filamentous fungi. Coupling polycistronic expression to multiplexed, markerless, CRISPR/Cas9-based genome editing, we develop a strategy termed HACKing (Highly efficient and Accessible system by CracKing genes into the genome) for the assembly of multigene pathways. HACKing allows the expression level of each enzyme to be precalibrated by linking their translation to those of host proteins with predetermined abundances under the desired fermentation conditions. We validate HACKing by rapidly constructing highly efficient Saccharomyces cerevisiae cell factories that express 13 biosynthetic genes, and produce model endogenous (1,090.41 ± 80.92 mg L −1 squalene) or heterologous (1.04 ± 0.02 mg L −1 mogrol) terpenoid products. Thus, HACKing addresses the need of synthetic biology for predictability, simplicity, scalability, and speed upon fungal pathway engineering for valuable metabolites.
研究领域:
合成生物学
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分子生物学
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基因工程
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代谢工程
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DOI
PubMed
高影响因子
BMC IMMUNOLOGY
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2023
·Vol. 24
·期 1
·1-12
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IF 3
Cai Jing,Wu Hao,Wang Chenxing,Chen Yujiao,Zhang Dingli,Guan Shiwei,Fu Beilei,Jin Yingli,Qian Cao
Inflammatory bowel disease (IBD) is a common immune-mediated condition with its molecular pathogenesis remaining to be fully elucidated. This study aimed to deepen our understanding of the role of FUT2 in human IBD, by studying a new surrogate gene Sec1, a neighboring gene of Fut2 and Fut1 that co-encodes the α 1,2 fucosyltransferase in mice. CRISPR/Cas9 was used to prepare Sec1 knockout (Sec1−/−) mice. IBD was induced in mice using 3% w/v dextran sulphate sodium. Small interfering RNA (siRNA) was employed to silence Sec1 in murine colon cancer cell lines CT26.WT and CMT93. IBD-related symptoms, colonic immune responses, proliferation and apoptosis of colon epithelial cells were assessed respectively to determine the role of Sec1 in mouse IBD. Impact of Sec1 on the expression of death receptor 5 (DR5) and other apoptosis-associated proteins were determined. Sec1 knockout was found to be associated with deterioration of IBD in mice and elevated immune responses in the colonic mucosa. Silencing Sec1 in CT26.WT and CMT93 cells led to greater secretion of inflammatory cytokines IL-1β, IL-6 and TNF-α. Cell counting kit 8 (CCK8) assay, flow cytometry and TUNEL detection suggested that Sec1 expression promoted the proliferation of colon epithelial cells, inhibited cell apoptosis, reduced cell arrest in G0/G1 phase and facilitated repair of inflammatory injury. Over-expression of DR5 and several apoptosis-related effector proteins was noticed in Sec1−/− mice and Sec1-silenced CT26.WT and CMT93 cells, supporting a suppressive role of Sec1 in cell apoptosis. Our results depicted important regulatory roles of Sec1 in mouse IBD, further reflecting the importance of FUT2 in the pathogenesis of human IBD.
研究领域:
免疫学
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分子生物学
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胃肠病学
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产品关联
DOI
PubMed
高影响因子
JOURNAL OF CONTROLLED RELEASE
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2024
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IF 10.5
Wenyan She,Haimei Li,Zichen Wang,Tingting Liu,Dongli Zhao,Zhibin Guo,Yujiao Liu,Yi Liu
Metabolic heterogeneity and the tumor immunosuppressive microenvironment (TIME) of triple-negative breast cancer (TNBC) hinder therapeutic effectiveness. Although emerging metabolic therapy and immunotherapy show promise, they are limited by off-target effects and immune escape. Here, a redox-activatable, sequentially-releasing nanoparticle (AMANC@M) for tumor-targeted delivery of anticancer agents and CRISPR/Cas9 has been developed. AMANC@M can reverse the TIME through dual metabolic inhibition, thereby enhancing TNBC therapy. AMANC@M demonstrates excellent biosafety and targets tumors precisely through biomimetic hybrid membrane-mediated homologous homing and the enhanced permeability and retention (EPR) effect. Once internalized into tumor cells, the CRISPR/Cas9 system (“energy nanolock”) is released through glutathione (GSH) cleavage and effectively knocks down the expression of lactate dehydrogenase A (LDHA) to suppress glycolysis. After peeling off of the gene editing shell, a newly synthesized targeted drug, CPI-Z2 (“nutrihijacker” and “energy nanolock”), is released in a controlled manner to block the mitochondrial tricarboxylic acid (TCA) cycle. Nitric oxide (NO) produced from loaded L-arginine enhances the efficiency of CPI-Z2 and reduces drug resistance. Combined with NO therapy, both blockades of nutrients and energy production transform the hypoxia and acidic TIME into an immunocompetent tumor microenvironment (TME) for tumor elimination. Furthermore, AMANC@M offers capabilities for photothermal (PT) therapy and provides clear imaging through PT, photoacoustic (PA), or computed tomography (CT) signals in tumor tissue. Thus, this study provides a new and promising sequentially stimuli-responsive targeting strategy for nanoparticle development, making it a potential treatment candidate for TNBC and other tumors.
研究领域:
肿瘤学
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纳米技术
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免疫学
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代谢工程
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生物医学工程
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DOI
PubMed
高影响因子
CELL
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2025
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IF 42.5
Ziqiang Zhou,Shicong Zhu,Yaqiang Hong,Guangpu Jin,Rui Ma,Fan Lin,Yiyang Zhang,Hsiang-Ying Lee,Nian Liu
Discrete genomic units can recombine into composite transposons that transcribe and transpose as single units, but their regulation and function are not fully understood. We report that composite transposons harbor bivalent histone marks, with activating and repressive marks in distinct regions. Genome-wide CRISPR-Cas9 screening, using a reporter driven by the hominid-specific composite transposon SVA (SINE [short interspersed nuclear element]-VNTR [variable number of tandem repeats]-Alu) in human cells, identified diverse genes that modify bivalent histone marks to regulate SVA transcription. SVA transcripts are critical for SVA’s cis -regulatory function in selectively contacting and activating long-range gene expression. Remarkably, a subset of bivalent SVAs is activated during erythropoiesis to boost multiple erythroid gene expression, and knocking down these SVAs leads to deficient erythropoiesis. The RNA-dependent cis -regulatory function of SVA activates genes for myelopoiesis and can contribute to aging-associated myeloid-biased hematopoiesis. These results reveal that the cis -regulatory functions of composite transposons are bivalently regulated to control cell fate transitions in development and aging.
研究领域:
分子生物学
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遗传学
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表观遗传学
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发育生物学
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细胞生物学
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血液学
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衰老研究
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产品关联
DOI
PubMed
高影响因子
ANALYST
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2020
·Vol. 145
·期 10
·3569-3574
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IF 3.978
Rui Guo,Shanwen Hu,Zonghua Wang
CRISPR/Cas9 has become a powerful tool for genomic manipulation, and the evaluation of the Cas9 activity is essential for the precise control of the CRISPR system. Herein, we develop a point-of-care platform for the rapid and visible determination of the Cas9 activity. A bipolar electrochemiluminescence (ECL) biosensor platform comprises an Au electric circuit fabricated on a glass substrate and the PDMS layer acts as a reservoir. DNA probes are then modified on electrodes and hybridization chain reaction (HCR) is applied to introduce ferrocene-labeled DNA. The CRISPR/Cas9 system can recognize the immobilized DNA probes and cleave them from the electrode surface as well as the labeled H1 and H2. Therefore, the cleavage activity is closely related to the labeled ferrocene. The modified electrode is then embodied in a closed bipolar system such that the oxidation reaction on sensing poles could be detected by the anodic ECL reactions on isolated luminescent poles due to charge balance, leading to the changes in ECL signals. This portable, integrated and convenient platform may become a meaningful tool for the discovery of a new CRISPR/Cas9 system or additional Cas9 inhibitors.
研究领域:
生物技术
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分子生物学
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分析化学
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DOI
PubMed
高影响因子
Nature Communications
·
2018
·Vol. 9
·期 1
·1-15
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IF 12.353
Usman Waqas Muhammad,Pham Tin Chanh,Kwok Yuk Yan,Vu Luyen Tien,Ma Victor,Peng Boya,Chan Yuen San,Wei Likun,Chin Siew Mei,Azad Ajijur,He Alex Bai-Liang,Leung Anskar Y. H.,Yang Mengsu,Shyh-Chang Ng,Cho William C.,Shi Jiahai,Le Minh T. N.
Most of the current methods for programmable RNA drug therapies are unsuitable for the clinic due to low uptake efficiency and high cytotoxicity. Extracellular vesicles (EVs) could solve these problems because they represent a natural mode of intercellular communication. However, current cellular sources for EV production are limited in availability and safety in terms of horizontal gene transfer. One potentially ideal source could be human red blood cells (RBCs). Group O-RBCs can be used as universal donors for large-scale EV production since they are readily available in blood banks and they are devoid of DNA. Here, we describe and validate a new strategy to generate large-scale amounts of RBC-derived EVs for the delivery of RNA drugs, including antisense oligonucleotides, Cas9 mRNA, and guide RNAs. RNA drug delivery with RBCEVs shows highly robust microRNA inhibition and CRISPR–Cas9 genome editing in both human cells and xenograft mouse models, with no observable cytotoxicity.
研究领域:
药理学
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分子生物学
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基因治疗
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生物技术
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产品关联
DOI
PubMed
高影响因子
Nano Today
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2021
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IF 20.722
Meng Lin,Zhenzhen Yang,Yiliang Yang,Yiwei Peng,Jiajia Li,Yitian Du,Qi Sun,Datong Gao,Quan Yuan,Yu Zhou,Xinyi Chen,Xianrong Qi
Tumor-associated macrophages (TAMs) are abundant in the tumor microenvironment and promote the tumor progression via multiple mechanisms. CD47 is overexpressed in most malignant tumors and acts as a “don’t eat me” signal to inhibit phagocytosis . We utilized CRISPR/Cas9 technology to knock out CD47 to guarantee the long-lasting anti-tumor immune responses. However, the reprogrammed TAMs are vulnerable to the inhibitory cytokines and tend to be transformed back into TAMs, and CD47 blockade alone may not be sufficient to elicit effective immune responses. We combined CD47 blockade with an immune-activating cytokine IL-12 for synergistic anti-tumor efficacy by genetically engineering the tumor cells into factories of IL-12 to in situ reprogram TAMs. Firstly, we designed a selective responsiveness accelerated gene delivery system named HPT-PFs that was dual modified with hyaluronic acid (HA) and tumor microenvironment sensitive peptides (TMSP) to simultaneously deliver plasmids for CD47 knockout and IL-12 production. Due to tumor-specific transfection and excellent endosome escape ability of HPT-PFs vector, more than 27% of tumor cells lost CD47 expression after HPT-PFs mediated gene editing, thus eliciting the phagocytosis by macrophages. And higher than 500 ng/ml of IL-12 was produced by tumor cells after HPT-PFs mediated pIL-12 expression, indicating the successful engineering of tumor cells into factories of IL-12. In melanoma-bearing mice models, drastic elevation of M1-polarized TAMs and secretion of inflammatory cytokines were observed when combined CD47 knockout with IL-12 production, which led to significant inhibition of tumor growth. Our study suggested that combination of CRISPR-mediated CD47 blockade with IL-12 production in tumor cells could synergistically promote macrophage-mediated immunotherapy, paving the way for CRISPR-based in situ engineering tumor cells for effective immunotherapy.
研究领域:
癌症生物学
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免疫学
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基因治疗
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生物技术
✓ 已验证
产品关联
DOI
高影响因子
Journal of Zhejiang University-SCIENCE B
·
2024
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IF 4.7
Jia Xiaodan,Lu Ke,Liang Xufang
Neuropeptide Y receptor Y8 (NPY8R) is a fish-specific receptor with two subtypes, NPY8AR and NPY8BR. Changes in expression levels during physiological processes or in vivo regulation after ventricular injection suggest that NPY8BR plays an important role in feeding regulation; this has been found in only a few fish, at present. In order to better understand the physiological function of npy8br , especially in digestion, we used clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) technology to generate npy8br −/− Japanese medaka ( Oryzias latipes ). We found that the deletion of npy8br in medaka larvae affected their feeding and digestion ability, ultimately affecting their growth. Specifically, npy8br deficiency in medaka larvae resulted in decreased feed intake and decreased expression levels of orexigenic genes ( npy and agrp ). npy8br −/− medaka larvae fed for 10 d (10th day of feeding) still had incompletely digested brine shrimp ( Artemia nauplii ) in the digestive tract 8 h after feeding, the messenger RNA (mRNA) expression levels of digestion-related genes ( amy, lpl, ctra , and ctrb ) were significantly decreased, and the activity of amylase, trypsin, and lipase also significantly decreased. The deletion of npy8br in medaka larvae inhibited the growth and significantly decreased the expression of growth-related genes ( gh and igf1 ). Hematoxylin and eosin (H&E) sections of intestinal tissue showed that npy8br −/− medaka larvae had damaged intestine, thinned intestinal wall, and shortened intestinal villi. So far, this is the first npy8br gene knockout model established in fish and the first demonstration that npy8br plays an important role in digestion.
研究领域:
分子生物学
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遗传学
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水产养殖
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生理学
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DOI
PubMed
高影响因子
NUCLEIC ACIDS RESEARCH
·
2021
·Vol. 49
·期 21
·12048-12068
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IF 16.971
Jiang Zhuoran,Wang Chao,Wu Zixin,Chen Kun,Yang Wei,Deng Hexiang,Song Heng,Zhou Xiang
N6-methyladenosine (m6A) modification is the most extensively studied epigenetic modification due to its crucial role in regulating an array of biological processes. Herein, Bsu06560, formerly annotated as an adenine deaminase derived from Bacillus subtilis 168, was recognized as the first enzyme capable of metabolizing the epigenetic nucleoside N6-methyladenosine. A model of Bsu06560 was constructed, and several critical residues were putatively identified via mutational screening. Two mutants, F91L and Q150W, provided a superiorly enhanced conversion ratio of adenosine and N6-methyladenosine. The CRISPR-Cas9 system generated Bsu06560-knockout, F91L, and Q150W mutations from the B. subtilis 168 genome. Transcriptional profiling revealed a higher global gene expression level in BS-F91L and BS-Q150W strains with enhanced N6-methyladenosine deaminase activity. The differentially expressed genes were categorized using GO, COG, KEGG and verified through RT-qPCR. This study assessed the crucial roles of Bsu06560 in regulating adenosine and N6-methyladenosine metabolism, which influence a myriad of biological processes. This is the first systematic research to identify and functionally annotate an enzyme capable of metabolizing N6-methyladenosine and highlight its significant roles in regulation of bacterial metabolism. Besides, this study provides a novel method for controlling gene expression through the mutations of critical residues.
研究领域:
分子生物学
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表观遗传学
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微生物学
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基因组学
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生物化学
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DOI
PubMed
高影响因子
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