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1.
Am J Transl Res ; 16(4): 1393-1400, 2024.
Article in English | MEDLINE | ID: mdl-38715822

ABSTRACT

OBJECTIVES: To evaluate the diagnostic and prognostic value of insulin-like growth factor-1 (IGF-1), galactoagglutinin-3 (GAL-3), and pentamerin-3 (PTX-3) levels in elderly patients with chronic heart failure (CHF). METHODS: In this retrospective study, 107 elderly CHF patients treated in Xiangyang Central Hospital were designated as the observation group, and 60 healthy individuals were selected as the control group. The cardiac function indexes and serum IGF-1, Gal-3, and PTX-3 levels were compared between the two groups. Furthermore, the serum IGF-1, Gal-3, and PTX-3 levels in patients across different cardiac function grades were compared, as well as in patients with poor or favorable prognosis. Additionally, receiver operating characteristic (ROC) curve was adopted to explore the diagnostic value of serum IGF-1, Gal-3, and PTX-3 levels for senile CHF; and multivariate logistic regression analysis was used to screen the independent factors affecting patients' prognosis. RESULTS: The serum IGF-1 level was significantly lower, while the levels of Gal-3 and PTX-3 were significantly higher in the observation group than those of the control group (all P<0.05). The serum IGF-1 level in patients with cardiac function grade IV was lower than that of the patients with cardiac function grade II and III, while the levels of Gal-3 and PTX-3 were higher than those with cardiac function grade II and III (all P<0.05). The serum IGF-1 level in the patients with cardiac function grade III was lower than those with cardiac function grade II, while the levels of Gal-3 and PTX-3 were higher in patients with grade III than those with grade II (all P<0.05). The serum IGF-1 level was lower, while the levels of Gal-3 and PTX-3 were higher in the patients with poor prognosis than those with favorable prognosis (all P<0.05). CONCLUSION: In elderly CHF patients, IGF-1 level were decreases, while the levels of Gal-3 and PTX-3 were increase. These biomarkers show high sensitivity in diagnosing CHF and are closely linked to the prognosis, indicating their value for clinical assessment and management of CHF.

2.
Hortic Res ; 11(3): uhae035, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38544552

ABSTRACT

Tomato (Solanum lycopersicum) is a globally cultivated crop with great economic value. The exocarp determines the appearance of tomato fruit and protects it from various biotic and abiotic challenges at both pre-harvest and post-harvest stages. However, no tomato exocarp-specific promoter is currently available, which hinders exocarp-based genetic engineering. Here, we identified by RNA sequencing and reverse transcription-quantitative PCR analyses that the tomato gene SlPR10 (PATHOGENESIS RELATED 10) was abundantly and predominantly expressed in the exocarp. A fluorescent reporter expressed by a 2087-bp SlPR10 promoter (pSlPR10) was mainly detected in the exocarp of transgenic tomato plants of both Ailsa Craig and Micro-Tom cultivars. This promoter was further utilized for transgenic expression of SlANT1 and SlMYB31 in tomato, which are master regulators of anthocyanin and cuticular wax biosynthesis, respectively. pSlPR10-driven SlANT1 expression resulted in anthocyanin accumulation in the exocarp, conferring gray mold resistance and extended shelf life to the fruit, while SlMYB31 expression led to waxy thickening in the fruit skin, delaying water loss and also extending fruit shelf life. Intriguingly, pSlPR10 and two other weaker tomato exocarp-preferential promoters exhibited coincided expression specificities in the gynophore of transgenic Arabidopsis (Arabidopsis thaliana) plants, providing not only an inkling of evolutionary homology between tomato exocarp and Arabidopsis gynophore but also useful promoters for studying gynophore biology in Arabidopsis. Collectively, this work reports a desirable promoter enabling targeted gene expression in tomato exocarp and Arabidopsis gynophore and demonstrates its usefulness in genetic improvement of tomato fruit quality.

3.
Nat Plants ; 9(11): 1832-1847, 2023 11.
Article in English | MEDLINE | ID: mdl-37845337

ABSTRACT

Base editors (BEs) empower the efficient installation of beneficial or corrective point mutations in crop and human genomes. However, conventional BEs can induce unpredictable guide RNA (gRNA)-independent off-target edits in the genome and transcriptome due to spurious activities of BE-enclosing deaminases, and current improvements mostly rely on deaminase-specific mutagenesis or exogenous regulators. Here we developed a split deaminase for safe editing (SAFE) system applicable to BEs containing distinct cytidine or adenosine deaminases, with no need of external regulators. In SAFE, a BE was properly split at a deaminase domain embedded inside a Cas9 nickase, simultaneously fragmenting and deactivating both the deaminase and the Cas9 nickase. The gRNA-conditioned BE reassembly conferred robust on-target editing in plant, human and yeast cells, while minimizing both gRNA-independent and gRNA-dependent off-target DNA/RNA edits. SAFE also substantially increased product purity by eliminating indels. Altogether, SAFE provides a generalizable solution for BEs to suppress off-target editing and improve on-target performance.


Subject(s)
Alkanesulfonic Acids , Gene Editing , RNA, Guide, CRISPR-Cas Systems , Humans , RNA , Deoxyribonuclease I/genetics , CRISPR-Cas Systems
4.
Clin Pediatr (Phila) ; 62(8): 914-918, 2023 09.
Article in English | MEDLINE | ID: mdl-36661073

ABSTRACT

To understand the psychological effects on behavior of girls with idiopathic central precocious puberty (ICPP) and to explore the role of gonadotropin-releasing hormone analog (GnRHa) in the reversal or blocking of the negative psychological effects on behaviors of girls with ICPP. A total of 100 girls with ICPP diagnosed at the Department of Endocrinology of Jiangxi Children's Hospital were divided into the treatment group and observation group with 50 cases in each group. The control group consisted of 50 healthy girls examined at our hospital during the same period. The Achenbach Child Behavior Check List ([CBCL] for parents) was used to evaluate the psychological effects on behavior of the girls diagnosed with ICPP and the girls in the control group, and the scores of related behavioral factors were calculated. At the same time, the psychological effects on behaviors of the girls with ICPP treated with GnRHa were followed up. (1) There were 100 girls with ICPP and 30 with behavioral problems. There were 50 normal healthy girls (control group) with 3 cases of behavior problems. Of the 50 girls with ICPP, after treatment, 8 had behavioral issues. The rate of abnormal psychological effects on behavior in the group of girls with ICPP before treatment was significantly higher than in the control group (P < .01), and after treatment, the rate was lower than before treatment (P < .05). (2) The scores of depression, social withdrawal, poor communication, and school discipline violation in the ICPP group were higher than those in the control group, with a statistical significance (P < .01). (3) After 24 months of GnRHa treatment for girls in the ICPP group, the scores of 4 factors, including depression, social withdrawal, poor communication, and violation of discipline in the Achenbach CBCL, were significantly different before and after treatment (P < .05). (1) Girls with ICPP have low self-esteem, low self-confidence, high incidences of psychological effects on behavior problems, manifested in depression, withdrawal, poor communication, discipline violations, and other aspects; (2) GnRHa treatment can reverse the low self-esteem and low self-confidence of girls with ICPP to varying degrees.


Subject(s)
Problem Behavior , Puberty, Precocious , Child , Female , Humans , Puberty, Precocious/drug therapy , Gonadotropin-Releasing Hormone , Body Height
5.
IEEE J Biomed Health Inform ; 26(10): 5177-5188, 2022 10.
Article in English | MEDLINE | ID: mdl-35820011

ABSTRACT

Contrast-enhanced computed tomography (CE-CT) is the gold standard for diagnosing aortic dissection (AD). However, contrast agents can cause allergic reactions or renal failure in some patients. Moreover, AD diagnosis by radiologists using non-contrast-enhanced CT (NCE-CT) images has poor sensitivity. To address this issue, we propose a novel cascaded multi-task generative framework for AD detection using NCE-CT volumes. The framework includes a 3D nnU-Net and a 3D multi-task generative architecture (3D MTGA). Specifically, the 3D nnU-Net was employed to segment aortas from NCE-CT volumes. The 3D MTGA was then employed to simultaneously synthesize CE-CT volumes, segment true & false lumen, and classify the patient as AD or non-AD. A theoretical formulation demonstrated that the 3D MTGA could increase the Jensen-Shannon Divergence (JSD) between AD and non-AD for each NCE-CT volume, thus indirectly improving the AD detection performance. Experiments also showed that the proposed framework could achieve an average accuracy of 0.831, a sensitivity of 0.938, and an F1-score of 0.847 in comparison with seven state-of-the-art classification models used by three radiologists with junior, intermediate, and senior experiences, respectively. The experimental results indicate that the proposed framework obtains superior performance to state-of-the-art models in AD detection. Thus, it has great potential to reduce the misdiagnosis of AD using NCE-CT in clinical practice. The source codes and supplementary materials for our framework are available at https://github.com/yXiangXiong/CMTGF.


Subject(s)
Aortic Dissection , Contrast Media , Aortic Dissection/diagnostic imaging , Aorta , Humans , Tomography, X-Ray Computed/methods
6.
Plant Cell ; 34(10): 3915-3935, 2022 09 27.
Article in English | MEDLINE | ID: mdl-35866997

ABSTRACT

PICKLE (PKL) is a chromodomain helicase DNA-binding domain 3 (CHD3) chromatin remodeler that plays essential roles in controlling the gene expression patterns that determine developmental identity in plants, but the molecular mechanisms through which PKL is recruited to its target genes remain elusive. Here, we define a cis-motif and trans-acting factors mechanism that governs the genomic occupancy profile of PKL in Arabidopsis thaliana. We show that two homologous trans-factors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 physically interact with PKL in vivo, localize extensively to PKL-occupied regions in the genome, and promote efficient PKL recruitment at thousands of target genes, including those involved in seed maturation. Transcriptome analysis and genetic interaction studies reveal a close cooperation of VAL1/VAL2 and PKL in regulating gene expression and developmental fate. We demonstrate that this recruitment operates at two master regulatory genes, ABSCISIC ACID INSENSITIVE3 and AGAMOUS-LIKE 15, to repress the seed maturation program and ensure the seed-to-seedling transition. Together, our work unveils a general rule through which the CHD3 chromatin remodeler PKL binds to its target chromatin in plants.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Abscisic Acid/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Chromatin/genetics , Chromatin/metabolism , DNA/metabolism , DNA Helicases/genetics , DNA Helicases/metabolism , Gene Expression Regulation, Plant/genetics , Seeds/genetics , Trans-Activators/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism
7.
Small ; 18(24): e2201525, 2022 06.
Article in English | MEDLINE | ID: mdl-35560973

ABSTRACT

Limited permeability in solid tumors significantly restricts the anticancer efficacy of nanomedicines. Light-driven nanomotors powered by photothermal converting engines are appealing carriers for directional drug delivery and simultaneous phototherapy. Nowadays, it is still a great challenge to construct metal-free photothermal nanomotors for a programmable anticancer treatment. Herein, one kind of photoactivated organic nanomachines is reported with asymmetric geometry assembled by light-to-heat converting semiconducting polymer engine and macromolecular anticancer payload through a straightforward nanoprecipitation process. The NIR-fueled polymer engine can be remotely controlled to power the nanomachines for light-driven thermophoresis in the liquid media and simultaneously thermal ablating the cancer cells. The great manipulability of the nanomachines allows for programming of their self-propulsion in the tumor microenvironment for effectively improving cellular uptake and tumor penetration of the anticancer payload. Taking the benefit from this behavior, a programmed treatment process is established at a low drug dose and a low photothermal temperature for significantly enhancing the antitumor efficacy.


Subject(s)
Nanoparticles , Neoplasms , Drug Delivery Systems , Humans , Phototherapy , Polymers , Tumor Microenvironment
8.
Nucleic Acids Res ; 50(6): 3565-3580, 2022 04 08.
Article in English | MEDLINE | ID: mdl-35286371

ABSTRACT

CRISPR/Cas-derived base editing tools empower efficient alteration of genomic cytosines or adenines associated with essential genetic traits in plants and animals. Diversified target sequences and customized editing products call for base editors with distinct features regarding the editing window and target scope. Here we developed a toolkit of plant base editors containing AID10, an engineered human AID cytosine deaminase. When fused to the N-terminus or C-terminus of the conventional Cas9 nickase (nSpCas9), AID10 exhibited a broad or narrow activity window at the protospacer adjacent motif (PAM)-distal and -proximal protospacer, respectively, while AID10 fused to both termini conferred an additive activity window. We further replaced nSpCas9 with orthogonal or PAM-relaxed Cas9 variants to widen target scopes. Moreover, we devised dual base editors with AID10 located adjacently or distally to the adenine deaminase ABE8e, leading to juxtaposed or spaced cytosine and adenine co-editing at the same target sequence in plant cells. Furthermore, we expanded the application of this toolkit in plants for tunable knockdown of protein-coding genes via creating upstream open reading frame and for loss-of-function analysis of non-coding genes, such as microRNA sponges. Collectively, this toolkit increases the functional diversity and versatility of base editors in basic and applied plant research.


Subject(s)
CRISPR-Associated Protein 9 , Gene Editing , Adenine , Animals , CRISPR-Associated Protein 9/genetics , CRISPR-Associated Protein 9/metabolism , CRISPR-Cas Systems/genetics , Cytosine
9.
Annu Int Conf IEEE Eng Med Biol Soc ; 2021: 2914-2917, 2021 11.
Article in English | MEDLINE | ID: mdl-34891855

ABSTRACT

Aortic dissection (AD) is a rare but potentially fatal disease with high mortality. The aim of this study is to synthesize contrast enhanced computed tomography (CE-CT) images from non-contrast CT (NCE-CT) images for detecting aortic dissection. In this paper, a cascaded deep learning framework containing a 3D segmentation network and a synthetic network was proposed and evaluated. A 3D segmentation network was firstly used to segment aorta from NCE-CT images and CE-CT images. A conditional generative adversarial network (CGAN) was subsequently employed to map the NCE-CT images to the CE-CT images non-linearly for the region of aorta. The results of the experiment suggest that the cascaded deep learning framework can be used for detecting the AD and outperforms CGAN alone.


Subject(s)
Aortic Dissection , Deep Learning , Aortic Dissection/diagnostic imaging , Aorta , Humans , Tomography, X-Ray Computed
10.
Biomed Res Int ; 2021: 4989297, 2021.
Article in English | MEDLINE | ID: mdl-34950733

ABSTRACT

OBJECTIVE: Deep vein thrombosis (DVT) is the third-largest cardiovascular disease, and accurate segmentation of venous thrombus from the black-blood magnetic resonance (MR) images can provide additional information for personalized DVT treatment planning. Therefore, a deep learning network is proposed to automatically segment venous thrombus with high accuracy and reliability. METHODS: In order to train, test, and external test the developed network, total images of 110 subjects are obtained from three different centers with two different black-blood MR techniques (i.e., DANTE-SPACE and DANTE-FLASH). Two experienced radiologists manually contoured each venous thrombus, followed by reediting, to create the ground truth. 5-fold cross-validation strategy is applied for training and testing. The segmentation performance is measured on pixel and vessel segment levels. For the pixel level, the dice similarity coefficient (DSC), average Hausdorff distance (AHD), and absolute volume difference (AVD) of segmented thrombus are calculated. For the vessel segment level, the sensitivity (SE), specificity (SP), accuracy (ACC), and positive and negative predictive values (PPV and NPV) are used. RESULTS: The proposed network generates segmentation results in good agreement with the ground truth. Based on the pixel level, the proposed network achieves excellent results on testing and the other two external testing sets, DSC are 0.76, 0.76, and 0.73, AHD (mm) are 4.11, 6.45, and 6.49, and AVD are 0.16, 0.18, and 0.22. On the vessel segment level, SE are 0.95, 0.93, and 0.81, SP are 0.97, 0.92, and 0.97, ACC are 0.96, 0.94, and 0.95, PPV are 0.97, 0.82, and 0.96, and NPV are 0.97, 0.96, and 0.94. CONCLUSIONS: The proposed deep learning network is effective and stable for fully automatic segmentation of venous thrombus on black blood MR images.


Subject(s)
Magnetic Resonance Imaging/methods , Thrombosis/diagnostic imaging , Veins/diagnostic imaging , Deep Learning , Humans , Image Processing, Computer-Assisted/methods , Neural Networks, Computer , Reproducibility of Results
11.
Asia Pac Psychiatry ; 13(2): e12422, 2021 Jun.
Article in English | MEDLINE | ID: mdl-33053613

ABSTRACT

INTRODUCTION: A family history of psychiatric disorders is one of the strongest risk factors for schizophrenia. The characteristics of patients with a family history of psychiatric disorders have not been systematically evaluated. METHODS: This multicenter study (26 centers, 2425 cases) was performed in a Chinese population to examine the sociodemographic and clinical characteristics of schizophrenia patients with a family history of psychotic disorders in comparison with those of patients with sporadic schizophrenia. RESULTS: Nineteen percent of patients had a family history of mental disease. Multiple logistic regression analysis revealed that ≥4 hospitalizations (OR = 1.78, P = .004), tobacco dependence (OR = 1.48, P = .006), alcohol dependence (OR = 1.74, P = .013), and physical illness (OR = 1.89, P = .001) were independently and significantly associated with a family history of mental disease. CONCLUSION: Patients with a family history of mental disorders present different demographics and clinical features than patients without a family history of psychiatric disorders.


Subject(s)
Psychotic Disorders , Schizophrenia , Hospitalization , Humans , Psychotic Disorders/epidemiology , Psychotic Disorders/genetics , Risk Factors , Schizophrenia/epidemiology , Schizophrenia/genetics
12.
J Integr Plant Biol ; 63(4): 634-645, 2021 Apr.
Article in English | MEDLINE | ID: mdl-33058471

ABSTRACT

Synthetic gene activators consisting of nuclease-dead Cas9 (dCas9) for single-guide RNA (sgRNA)-directed promoter binding and a transcriptional activation domain (TAD) represent new tools for gene activation from endogenous genomic locus in basic and applied plant research. However, multiplex gene coactivation by dCas9-TADs has not been demonstrated in whole plants. There is also room to optimize the performance of these tools. Here, we report that our previously developed gene activator, dCas9-TV, could simultaneously upregulate OsGW7 and OsER1 in rice by up to 3,738 fold, with one sgRNA targeting to each promoter. The gene coactivation could persist to at least the fourth generation. Astonishingly, the polycistronic tRNA-sgRNA expression under the maize ubiquitin promoter, a Pol II promoter, could cause enormous activation of these genes by up to >40,000-fold in rice. Moreover, the yeast GCN4 coiled coil-mediated dCas9-TV dimerization appeared to be promising for enhancing gene activation. Finally, we successfully introduced a self-amplification loop for dCas9-TV expression in Arabidopsis to promote the transcriptional upregulation of AtFLS2, a previously characterized dCas9-TV-refractory gene with considerable basal expression. Collectively, this work illustrates the robustness of dCas9-TV in multigene coactivation and provides broadly useful strategies for boosting transcriptional activation efficacy of dCas9-TADs in plants.


Subject(s)
CRISPR-Cas Systems/physiology , Arabidopsis/genetics , Arabidopsis/metabolism , CRISPR-Cas Systems/genetics , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , Promoter Regions, Genetic/genetics , RNA, Guide, Kinetoplastida/genetics
13.
Cytogenet Genome Res ; 160(10): 565-578, 2020.
Article in English | MEDLINE | ID: mdl-33022677

ABSTRACT

The excessive production of inflammatory mediators by vascular endothelial cells (ECs) greatly contributes to the development of atherosclerosis. In this study, we explored the potential effect of lncRNA MALAT1 on endothelial inflammation. First, the EC inflammation model was constructed by treating human umbilical vein ECs (HUVECs) and human coronary artery ECs (HCAECs) with oxidized low-density lipoprotein (ox-LDL), which confirmed the role of MALAT1 in the inflammatory activity. Then MALAT1 was overexpressed in HUVECs and HCAECs, and the levels of inflammatory mediators and nitric oxide (NO) were examined by Western blotting, ELISA, and NO detection assay. The migration ability was confirmed by wound healing assay. The interactions among MALAT1, miR-590, and STAT3 were predicted by bioinformatics analysis and verified by qRT-PCR, Western blotting, or dual-luciferase reporter assay. MALAT1 was upregulated in ECs treated with ox-LDL, and knockdown of MALAT1 significantly inhibited ox-LDL-induced inflammation. MALAT1 overexpression potentiated the inflammatory activities of ECs, including enhanced production of inflammatory cytokines (IL-6, IL-8, and TNF-α) and adhesion molecules (VCAM1 and ICAM1), and decreased NO level and cell migratory ability. Mechanistically, MALAT1 could directly downregulate miR-590, and miR-590 could bind to the 3'-UTR of STAT3 to repress its expression. Additionally, overexpression of MALAT1-mediated inflammation was largely abrogated by the concomitant overexpression of miR-590. miR-590 knockdown activated the inflammatory response, which was reversed by STAT3 inhibition. Thus, MALAT1 serves as a proinflammatory lncRNA in ECs through regulating the miR-590/STAT3 axis, suggesting that MALAT1 may be a promising therapeutic target during the treatment of atherosclerosis.


Subject(s)
Endothelial Cells/metabolism , Endothelial Cells/pathology , Inflammation/genetics , MicroRNAs/metabolism , RNA, Long Noncoding/metabolism , STAT3 Transcription Factor/metabolism , 3' Untranslated Regions/genetics , Base Sequence , Endothelial Cells/drug effects , Gene Expression Regulation/drug effects , Gene Knockdown Techniques , Human Umbilical Vein Endothelial Cells/metabolism , Human Umbilical Vein Endothelial Cells/pathology , Humans , Inflammation/pathology , Lipoproteins, LDL/pharmacology , MicroRNAs/genetics , Models, Biological , Phenotype , Protein Binding/genetics , RNA, Long Noncoding/genetics
14.
aBIOTECH ; 1(1): 32-40, 2020 Jan.
Article in English | MEDLINE | ID: mdl-36305006

ABSTRACT

Targeted gene manipulation is highly desirable for fundamental plant research, plant synthetic biology, and molecular breeding. The clustered regularly interspaced short palindromic repeats-associated (Cas) nuclease is a revolutionary tool for genome editing, and has received snowballing popularity for gene knockout applications in diverse organisms including plants. Recently, the nuclease-dead Cas (dCas) proteins have been repurposed as programmable transcriptional regulators through translational fusion with portable transcriptional repression or activation domains, which has paved new ways for flexible and multiplex control over the activities of target genes of interest without the need to generate DNA lesions. Here, we review the most important breakthroughs of dCas transcriptional regulators in non-plant organisms and recent accomplishments of this growing field in plants. We also provide perspectives on future development directions of dCas transcriptional regulators in plant research in hope to stimulate their quick evolution and broad applications.

15.
Biochem Biophys Res Commun ; 521(2): 478-484, 2020 01 08.
Article in English | MEDLINE | ID: mdl-31677796

ABSTRACT

The prognosis for hepatocellular carcinoma (HCC) is dismal. Long noncoding RNA PVT1 has been linked to malignancies and might be a deleterious therapy target. However, the key events controlling its expression in HCC remain undetermined. Here, we address how PVT1 is fine-regulated and its downstream signaling in hepatoma cells. Interestingly, we found that c-Myc and P53 could divergently regulate PVT1 transcription. Oncoprotein c-Myc enhances PVT1 expression, whereas P53 suppresses its expression. We also identified miR-214 as a crucial, negative regulator of PVT1. Consistently, high miR-214 levels were significantly correlated with diminished PVT1 expression in HCC specimens. Silencing of PVT1 by ectopic miR-214 or siRNAs markedly inhibited viability and invasion of HCC cells. In opposition, inhibition of endogenous miR-214 promoted PVT1 expression and enhanced cell proliferation. Notably, oncogenic GDF15 is a potential downstream target of the miR-214-PVT1 signaling. Collectively, our results show that the c-Myc/P53/miR-214-PVT1-GDF15 axis is implicated in HCC development, shedding light on the mechanistic actions of PVT1 and representing potential targets for HCC clinical intervention.


Subject(s)
Carcinoma, Hepatocellular/pathology , Growth Differentiation Factor 15/antagonists & inhibitors , Liver Neoplasms/pathology , MicroRNAs/physiology , RNA, Long Noncoding/antagonists & inhibitors , Carcinogenesis/drug effects , Cell Proliferation , Gene Silencing , Humans , Proto-Oncogene Proteins c-myc/metabolism , RNA, Small Interfering/pharmacology , Signal Transduction , Tumor Suppressor Protein p53/metabolism
16.
New Phytol ; 222(2): 1139-1148, 2019 04.
Article in English | MEDLINE | ID: mdl-30565255

ABSTRACT

Gene knockout tools are highly desirable for basic and applied plant research. Here, we leverage the Cas9-derived cytosine base editor to introduce precise C-to-T mutations to disrupt the highly conserved intron donor site GT or acceptor site AG, thereby inducing messenger RNA (mRNA) missplicing and gene disruption. As proof of concept, we successfully obtained Arabidopsis null mutant of MTA gene in the T2 generation and rice double null mutant of GL1-1 and NAL1 genes in the T0 generation by this strategy. Elimination of the original intron donor site or acceptor site could trigger aberrant splicing at a new specific exonic site, but not at the closest GT or AG site, suggesting cryptic rules governing splice site recognition. The strategy presented expands the applications of base editing technologies in plants by providing a new means for gene inactivation without generating DNA double-strand breaks, and it can potentially serve as a useful tool for studying the biology of mRNA splicing.


Subject(s)
Arabidopsis/genetics , Oryza/genetics , RNA Editing/genetics , RNA Splicing/genetics , Base Sequence , Introns/genetics , Plants, Genetically Modified , RNA Splice Sites/genetics
18.
Nat Plants ; 3(12): 930-936, 2017 Dec.
Article in English | MEDLINE | ID: mdl-29158545

ABSTRACT

Overexpression of complementary DNA represents the most commonly used gain-of-function approach for interrogating gene functions and for manipulating biological traits. However, this approach is challenging and inefficient for multigene expression due to increased labour for cloning, limited vector capacity, requirement of multiple promoters and terminators, and variable transgene expression levels. Synthetic transcriptional activators provide a promising alternative strategy for gene activation by tethering an autonomous transcription activation domain (TAD) to an intended gene promoter at the endogenous genomic locus through a programmable DNA-binding module. Among the known custom DNA-binding modules, the nuclease-dead Streptococcus pyogenes Cas9 (dCas9) protein, which recognizes a specific DNA target through base pairing between a synthetic guide RNA and DNA, outperforms zinc-finger proteins and transcription activator-like effectors, both of which target through protein-DNA interactions 1 . Recently, three potent dCas9-based transcriptional activation systems, namely VPR, SAM and SunTag, have been developed for animal cells 2-6 . However, an efficient dCas9-based transcriptional activation platform is still lacking for plant cells 7-9 . Here, we developed a new potent dCas9-TAD, named dCas9-TV, through plant cell-based screens. dCas9-TV confers far stronger transcriptional activation of single or multiple target genes than the routinely used dCas9-VP64 activator in both plant and mammalian cells.


Subject(s)
Bacterial Proteins/genetics , Endonucleases/genetics , Mammals/genetics , Plants/genetics , Transcriptional Activation/genetics , Animals , Arabidopsis/genetics , CRISPR-Associated Protein 9 , Genetic Techniques , Humans , Transcription Initiation Site
19.
Oncotarget ; 7(35): 56501-56507, 2016 Aug 30.
Article in English | MEDLINE | ID: mdl-27489354

ABSTRACT

Accumulated evidences demonstrated that GLB1 is involved in cell senescence and cancer development. The GLB1 rs4678680 single nucleotide polymorphism (SNP) has been identified as a hepatocellular carcinoma (HCC) susceptibility polymorphism by a genome-wide association study in Korean population previously. However, little or nothing was known about its involvement and functional significance in hepatitis B viruses (HBV)-related HCC in Chinese. Therefore, we investigated the association between the GLB1 rs4678680 SNP and HBV-related HCC risk as well as its biological function in vivo. Genotypes were determined in two independent case-control sets from two medical centers of China. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated by logistic regression. The potential regulation role the rs4678680 genetic variant on GLB1 expression was examined with HCC and normal liver tissues. We found that The rs4678680 G allele was showed to be risk allele; individuals with the TG genotype had an OR of 1.51 (95% CI = 1.10-2.07, P = 0.010, Shandong set) or 1.49 (95% CI = 1.11-1.99, P = 0.008, Jiangsu set) for developing HBV-related HCC, respectively, compared with individuals with the TT genotype. This association was more pronounced in males, individuals aged older than 57 years and drinkers (all P < 0.05). In the genotype-phenotype correlation analyses of fifty-six human liver tissue samples, rs4678680 TG or GG was associated with a statistically significant increase of GLB1 mRNA expression (P < 0.05). Our data indicated that the GLB1 rs4678680 SNP contributes to susceptibility to develop HBV-related HCC, highlighting the involvement of GLB1 and cell senescence in etiology of HCC.


Subject(s)
Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/virology , Hepatitis B, Chronic/genetics , Liver Neoplasms/genetics , Liver Neoplasms/virology , beta-Galactosidase/genetics , Aged , Alcohol Drinking , Alleles , Asian People/genetics , China , Female , Gene Expression Profiling , Gene Frequency , Genetic Association Studies , Genetic Predisposition to Disease , Genotype , Hepatitis B virus , Humans , Male , Middle Aged , Odds Ratio , Polymorphism, Single Nucleotide , Risk
20.
Sci Rep ; 6: 27013, 2016 06 01.
Article in English | MEDLINE | ID: mdl-27245877

ABSTRACT

Metallopeptidase 13 (MMP13), a well-known and highly regulated zinc-dependent MMP collagenase, plays a crucial part in development and progression of esophageal squamous cell carcinoma (ESCC). Therefore, we examined associations between ESCC susceptibility and four haplotype-tagging single nucleotide polymorphisms (htSNPs) using a two stage case-control strategy. Odds ratios (OR) and 95% confidence intervals (95% CI) were computed by logistic regression model. After analyzing 1588 ESCC patients and frequency-matched 1600 unaffected controls, we found that MMP13 rs2252070 G > A genetic polymorphism is significantly associated with ESCC risk in Chinese Han populations (GA: OR = 0.63, 95% CI = 0.54-0.74, P = 1.7 × 10(-6), AA: OR = 0.73, 95% CI = 0.66-0.81, P = 1.8 × 10(-6)). Interestingly, the rs2252070 G-to-A change was shown to diminish a Sp1-binding site in ESCC cells. Reporter gene assays indicated that the rs2252070 A allele locating in a potential MMP13 promoter has low promoter activities. After measuring MMP13 gene expression in sixty-six pairs of esophageal cancer and normal tissues, we observed that the rs2252070 A protective allele carriers showed decreased oncogene MMP13 expression. Results of these analyses underline the support of the notion that MMP13 might function as a key oncogene in esophageal carcinogenesis.


Subject(s)
Carcinoma, Squamous Cell/genetics , Esophageal Neoplasms/genetics , Gene Expression Regulation, Neoplastic , Genetic Predisposition to Disease , Matrix Metalloproteinase 13/genetics , Polymorphism, Single Nucleotide , Sp1 Transcription Factor/genetics , Adult , Alleles , Asian People , Base Sequence , Binding Sites , Carcinoma, Squamous Cell/ethnology , Carcinoma, Squamous Cell/metabolism , Carcinoma, Squamous Cell/pathology , Case-Control Studies , Esophageal Neoplasms/ethnology , Esophageal Neoplasms/metabolism , Esophageal Neoplasms/pathology , Esophageal Squamous Cell Carcinoma , Female , Gene Frequency , Haplotypes , Humans , Male , Matrix Metalloproteinase 13/metabolism , Middle Aged , Odds Ratio , Promoter Regions, Genetic , Risk Factors , Sp1 Transcription Factor/metabolism
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