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1.
Fa Yi Xue Za Zhi ; 40(1): 37-42, 2024 Feb 25.
Article in English, Chinese | MEDLINE | ID: mdl-38500459

ABSTRACT

OBJECTIVES: To investigate the toxicokinetic differences of 3,4-methylenedioxy-N-methylamphetamine (MDMA) and its metabolite 4,5-methylene dioxy amphetamine (MDA) in rats after single and continuous administration of MDMA, providing reference data for the forensic identification of MDMA. METHODS: A total of 24 rats in the single administration group were randomly divided into 5, 10 and 20 mg/kg experimental groups and the control group, with 6 rats in each group. The experimental group was given intraperitoneal injection of MDMA, and the control group was given intraperitoneal injection of the same volume of normal saline as the experimental group. The amount of 0.5 mL blood was collected from the medial canthus 5 min, 30 min, 1 h, 1.5 h, 2 h, 4 h, 6 h, 8 h, 10 h, 12 h after administration. In the continuous administration group, 24 rats were randomly divided into the experimental group (18 rats) and the control group (6 rats). The experimental group was given MDMA 7 d by continuous intraperitoneal injection in increments of 5, 7, 9, 11, 13, 15, 17 mg/kg per day, respectively, while the control group was given the same volume of normal saline as the experimental group by intraperitoneal injection. On the eighth day, the experimental rats were randomly divided into 5, 10 and 20 mg/kg dose groups, with 6 rats in each group. MDMA was injected intraperitoneally, and the control group was injected intraperitoneally with the same volume of normal saline as the experimental group. On the eighth day, 0.5 mL of blood was taken from the medial canthus 5 min, 30 min, 1 h, 1.5 h, 2 h, 4 h, 6 h, 8 h, 10 h, 12 h after administration. Liquid chromatography-triple quadrupole tandem mass spectrometry was used to detect MDMA and MDA levels, and statistical software was employed for data analysis. RESULTS: In the single-administration group, peak concentrations of MDMA and MDA were reached at 5 min and 1 h after administration, respectively, with the largest detection time limit of 12 h. In the continuous administration group, peak concentrations were reached at 30 min and 1.5 h after administration, respectively, with the largest detection time limit of 10 h. Nonlinear fitting equations for the concentration ratio of MDMA and MDA in plasma and administration time in the single-administration group and continuous administration group were as follows: T=10.362C-1.183, R2=0.974 6; T=7.397 3C-0.694, R2=0.961 5 (T: injection time; C: concentration ratio of MDMA to MDA in plasma). CONCLUSIONS: The toxicokinetic data of MDMA and its metabolite MDA in rats, obtained through single and continuous administration, including peak concentration, peak time, detection time limit, and the relationship between concentration ratio and administration time, provide a theoretical and data foundation for relevant forensic identification.


Subject(s)
3,4-Methylenedioxyamphetamine , Amphetamines , N-Methyl-3,4-methylenedioxyamphetamine , Rats , Animals , Amphetamine , N-Methyl-3,4-methylenedioxyamphetamine/toxicity , 3,4-Methylenedioxyamphetamine/analysis , Toxicokinetics , Saline Solution
2.
Appl Opt ; 63(4): 1125-1134, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38437411

ABSTRACT

A three-axis angle measurement method is proposed using an optical wedge as a reflector. In this paper, the mathematical model of three-axis angle solving corresponding to the method is derived, and it is verified and corrected by establishing an optical simulation model, and, finally, the feasibility and measurement accuracy of the method are verified by using a principle prototype. The experimental results show that the RMS values of the measurement errors of pitch angle α, yaw angle ß, and roll angle γ are 6.27 ' ' , 4.35 ' ' , and 17.68 ' ' , respectively, within the measurement range of ±2∘, and the measurement accuracy is insensitive to the measurement distance.

3.
Opt Express ; 31(23): 39140-39152, 2023 Nov 06.
Article in English | MEDLINE | ID: mdl-38018000

ABSTRACT

In this work, programmable optical switching integrated chips for 4-bit binary true/inverse/complement optical code conversions (OCCs) are proposed based on fluorinated photopolymers. Fluorinated bis-phenol-A novolac resin (FAR) with low absorption loss and fluorinated polyacrylate (FPA) with high thermal stability are self-synthesized as core and cladding layer, respectively. The basic architecture of operating unit for the photonic chip designed is composed of directional coupler Mach-Zehnder interferometer (DC-MZI) thermo-optic (TO) switching, X-junction, and Y-bunching waveguide structures. The waveguide module by cascading 16 operating units could realize OCCs function through optical transmission matrix. The response time of the 4-bit binary OCCs is measured as about 300 µs. The insertion loss and extinction ratio of the actual chip are obtained as about 10.5 dB and 15.2 dB, respectively. The electric driving power consumption for OCCs is less than 6 mW. The true/inverse/complement OCCs are achieved by the programmable modulation circuit. The proposed technique is suitable for achieving optical digital computing system with high-speed signal processing and low power consumption.

4.
J Hepatol ; 79(6): 1418-1434, 2023 12.
Article in English | MEDLINE | ID: mdl-37604269

ABSTRACT

BACKGROUND & AIMS: Integrin αv (ITGAV, CD51) is regarded as a key component in multiple stages of tumor progression. However, the clinical failure of cilengitide, a specific inhibitor targeting surface CD51, suggests the importance of yet-unknown mechanisms by which CD51 promotes tumor progression. METHODS: In this study, we used several hepatocellular carcinoma (HCC) cell lines and murine hepatoma cell lines. To investigate the role of CD51 on HCC progression, we used a 3D invasion assay and in vivo bioluminescence imaging. We used periostin-knockout transgenic mice to uncover the role of the tumor microenvironment on CD51 cleavage. Moreover, we used several clinically relevant HCC models, including patient-derived organoids and patient-derived xenografts, to evaluate the therapeutic efficacy of cilengitide in combination with the γ-secretase inhibitor LY3039478. RESULTS: We found that CD51 could undergo transmembrane cleavage by γ-secretase to produce a functional intracellular domain (CD51-ICD). The cleaved CD51-ICD facilitated HCC invasion and metastasis by promoting the transcription of oxidative phosphorylation-related genes. Furthermore, we identified cancer-associated fibroblast-derived periostin as the major driver of CD51 cleavage. Lastly, we showed that cilengitide-based therapy led to a dramatic therapeutic effect when supplemented with LY3039478 in both patient-derived organoid and xenograft models. CONCLUSIONS: In summary, we revealed previously unrecognized mechanisms by which CD51 is involved in HCC progression and uncovered the underlying cause of cilengitide treatment failure, as well as providing evidence supporting the translational prospects of combined CD51-targeted therapy in the clinic. IMPACT AND IMPLICATIONS: Integrin αv (CD51) is a widely recognized pro-tumoral molecule that plays a crucial role in various stages of tumor progression, making it a promising therapeutic target. However, despite early promising results, cilengitide, a specific antagonist of CD51, failed in a phase III clinical trial. This prompted further investigation into the underlying mechanisms of CD51's effects. This study reveals that the γ-secretase complex directly cleaves CD51 to produce an intracellular domain (CD51-ICD), which functions as a pro-tumoral transcriptional regulator and can bypass the inhibitory effects of cilengitide by entering the nucleus. Furthermore, the localization of CD51 in the nucleus is significantly associated with the prognosis of patients with HCC. These findings provide a theoretical basis for re-evaluating cilengitide in clinical settings and highlight the importance of identifying a more precise patient subpopulation for future clinical trials targeting CD51.


Subject(s)
Carcinoma, Hepatocellular , Integrin alphaV , Liver Neoplasms, Experimental , Liver Neoplasms , Animals , Humans , Mice , Amyloid Precursor Protein Secretases , Carcinoma, Hepatocellular/genetics , Cell Line, Tumor , Integrin alphaV/genetics , Integrin alphaV/metabolism , Liver Neoplasms/genetics , Tumor Microenvironment
5.
Soc Psychol Educ ; : 1-15, 2023 Mar 27.
Article in English | MEDLINE | ID: mdl-37362053

ABSTRACT

The changes that COVID-19 pandemic has brought upon the world are unprecedented. Its impact on students' learning is equally profound, making it critical to heed students' academic achievement effects that may derive from these alterations. Therefore, the present study explored an integrative model of mental health, self-regulated learning and academic achievement among adolescents during the pandemic. Participants were 1001 senior high school students (Mage = 17.00, SDage = 0.78, 48.7% female) from China. Results showed that the degree to which students were mentally healthy was not significantly related to academic achievement, whereas academic achievement and mental health were positively associated with self-regulated learning. Following structural equation modelling analysis, the effect of mental health on academic achievement was fully mediated by self-regulated learning. Taken together, the findings emphasised the necessity of developing self-regulated learning strategies during public health emergencies and have clinical and educational implications for planning psychological interventions in order to improve mental health and academic performance as well.

6.
Opt Express ; 31(12): 19415-19427, 2023 Jun 05.
Article in English | MEDLINE | ID: mdl-37381357

ABSTRACT

In this study, a triple-layered optical interconnecting integrated waveguide chip was designed and fabricated using an epoxy cross-linking polymer photonic platform. Fluorinated photopolymers FSU-8 and AF-Z-PC EP were self-synthesized as waveguide cores and cladding materials, respectively. The triple-layered optical interconnecting waveguide device comprised 4 × 4 arrayed waveguide grating (AWG) -based wavelength-selective switching (WSS) arrays, 4 × 4 multi-mode interference (MMI) -cascaded channel-selective switching (CSS) arrays, and 3 × 3 direct-coupling (DC) interlayered switching arrays. The overall optical polymer waveguide module was fabricated by direct UV writing. For the multilayered WSS arrays, the wavelength-shifting sensitivity was ∼0.48 nm/°C. For the multilayered CSS arrays, the average switching time was ∼280 µs, and the maximum power consumption was <30 mW. For interlayered switching arrays, the extinction ratio approximated 15.2 dB. The transmission loss for the triple-layered optical waveguide chip was measured as 10.0-12.1 dB. The flexible multilayered photonic integrated circuits (PIC) can be used in high-density integrated optical interconnecting systems with a large-volume optical information transmission capacity.

7.
J Chem Phys ; 158(20)2023 May 28.
Article in English | MEDLINE | ID: mdl-37212410

ABSTRACT

The complex phase diagram and bonding nature of the TiAl system make it difficult to accurately describe its various properties and phases by traditional atomistic force fields. Here, we develop a machine learning interatomic potential with a deep neural network method for the TiAlNb ternary alloy based on a dataset built by first-principles calculations. The training set includes bulk elementary metals and intermetallic structures with slab and amorphous configurations. This potential is validated by comparing bulk properties-including lattice constant and elastic constants, surface energies, vacancy formation energies, and stacking fault energies-with their respective density functional theory values. Moreover, our potential could accurately predict the average formation energy and stacking fault energy of γ-TiAl doped with Nb. The tensile properties of γ-TiAl are simulated by our potential and verified by experiments. These results support the applicability of our potential under more practical conditions.

8.
Article in English | MEDLINE | ID: mdl-35952936

ABSTRACT

Although the function of tRNA in the translational process is well established, it remains controversial whether tRNA abundance is tightly associated with translational efficiency (TE) in mammals. Moreover, how critically the expression of tRNAs contributes to the establishment of tissue-specific proteomes in mammals has not been well addressed. Here, we measured both tRNA expression using demethylase-tRNA sequencing (DM-tRNA-seq) and TE of mRNAs using ribosome-tagging sequencing (RiboTag-seq) in the brain, heart, and testis of mice. Remarkable variation in the expression of tRNA isodecoders was observed among different tissues. When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons, we observed an expected reduction in the variation of anticodon expression across all samples, an unexpected smaller variation of anticodon usage bias, and an unexpected larger variation of tRNA isotype expression at amino acid level. Regardless of whether or not they share the same anticodons, the isodecoders encoding the same amino acids are co-expressed across different tissues. Based on the expression of tRNAs and the TE of mRNAs, we find that the tRNA adaptation index (tAI) and TE are significantly correlated in the same tissues but not between tissues; and tRNA expression and the amino acid composition of translating peptides are positively correlated in the same tissues but not between tissues. We therefore hypothesize that the tissue-specific expression of tRNAs might be due to post-transcriptional mechanisms. This study provides a resource for tRNA and translation studies, as well as novel insights into the dynamics of tRNAs and their roles in translational regulation.

9.
Methods ; 203: 56-61, 2022 07.
Article in English | MEDLINE | ID: mdl-35306148

ABSTRACT

N6-methyladenosine (m6A) is a reversible and prevalent internal modification in RNAs and can be dynamically modulated by methyltransferase and demethylase. Targeted manipulation of m6A RNA modification is critical in studying the functions of specific m6A sites as well as developing molecular therapies through targeting m6A. The CRISPR-Cas systems including CRISPR-Cas9 and CRISPR-Cas13 have been widely used to edit and modify specific nucleotides on DNA and RNA through fusing effective proteins such as enzymes with Cas9/13. Through taking advantage of the m6A methyltransferase and demethylase, a series of CRISPR-Cas-based methods have also been developed to manipulate the m6A methylation at specific RNA sites. This review summarizes the latest CRISPR-Cas13 and Cas9 toolkits for m6A site-specific manipulation, including fundamental components, on-target efficiency, editing window, PAM/PFS requirement, and subcellularly localized targeting as well as potential limitations. We thus aim to provide an overview to assist researchers to choose an optimal tool to manipulate m6A for different purposes and also point out possible optimization strategies.


Subject(s)
CRISPR-Cas Systems , Gene Editing , CRISPR-Cas Systems/genetics , Gene Editing/methods , Methyltransferases/genetics , Methyltransferases/metabolism , RNA/genetics , RNA, Guide, Kinetoplastida/genetics , RNA, Guide, Kinetoplastida/metabolism
10.
Adv Sci (Weinh) ; 9(13): e2103357, 2022 May.
Article in English | MEDLINE | ID: mdl-35229495

ABSTRACT

Spintronic devices are considered as one of the most promising technologies for non-volatile memory and computing. However, two crucial drawbacks, that is, lack of intrinsic multi-level operation and low on/off ratio, greatly hinder their further application for advanced computing concepts, such as deep neural network (DNN) accelerator. In this paper, a spintronic multi-level memory unit with high on/off ratio is proposed by integrating several series-connected magnetic tunnel junctions (MTJs) with perpendicular magnetic anisotropy (PMA) and a Schottky diode in parallel. Due to the rectification effect on the PMA MTJ, an on/off ratio over 100, two orders of magnitude higher than intrinsic values, is obtained under proper proportion of alternating current and direct current. Multiple resistance states are stably achieved and can be reconfigured by spin transfer torque effect. A computing-in-memory architecture based DNN accelerator for image classification with the experimental parameters of this proposal to evidence its application potential is also evaluated. This work can satisfy the rigorous requirements of DNN for memory unit and promote the development of high-accuracy and robust artificial intelligence applications.

11.
Nanomaterials (Basel) ; 12(3)2022 Jan 28.
Article in English | MEDLINE | ID: mdl-35159791

ABSTRACT

Thermally conductive and electrically insulating materials have attracted much attention due to their applications in the field of microelectronics, but through-plane thermal conductivity of materials is still low at present. In this paper, a simple and environmentally friendly strategy is proposed to improve the through-plane thermal conductivity of epoxy composites using a 3D boron nitride (3D-BN) framework. In addition, the effect of filler sizes in 3D-BN skeletons on thermal conductivity was investigated. The epoxy composite with larger BN in lateral size showed a higher through-plane thermal conductivity of 2.01 W/m·K and maintained a low dielectric constant of 3.7 and a dielectric loss of 0.006 at 50 Hz, making it desirable for the application in microelectronic devices.

12.
Circulation ; 145(9): 675-687, 2022 03.
Article in English | MEDLINE | ID: mdl-35189703

ABSTRACT

BACKGROUND: High blood cholesterol accelerates the progression of atherosclerosis, which is an asymptomatic process lasting for decades. Rupture of atherosclerotic plaques induces thrombosis, which results in myocardial infarction or stroke. Lowering cholesterol levels is beneficial for preventing atherosclerotic cardiovascular disease. METHODS: Low-density lipoprotein (LDL) receptor (LDLR) was used as bait to identify its binding proteins in the plasma, and the coagulation factor prekallikrein (PK; encoded by the KLKB1 gene) was revealed. The correlation between serum PK protein content and lipid levels in young Chinese Han people was then analyzed. To investigate the effects of PK ablation on LDLR and lipid levels in vivo, we genetically deleted Klkb1 in hamsters and heterozygous Ldlr knockout mice and knocked down Klkb1 using adeno-associated virus-mediated shRNA in rats. The additive effect of PK and proprotein convertase subtilisin/kexin 9 inhibition also was evaluated. In addition, we applied the anti-PK neutralizing antibody that blocked the PK and LDLR interaction in mice. Mice lacking both PK and apolipoprotein e (Klkb1-/-Apoe-/-) were generated to assess the role of PK in atherosclerosis. RESULTS: PK directly bound LDLR and induced its lysosomal degradation. The serum PK concentrations positively correlated with LDL cholesterol levels in 198 young Chinese Han adults. Genetic depletion of Klkb1 increased hepatic LDLR and decreased circulating cholesterol in multiple rodent models. Inhibition of proprotein convertase subtilisin/kexin 9 with evolocumab further decreased plasma LDL cholesterol levels in Klkb1-deficient hamsters. The anti-PK neutralizing antibody could similarly lower plasma lipids through upregulating hepatic LDLR. Ablation of Klkb1 slowed the progression of atherosclerosis in mice on Apoe-deficient background. CONCLUSIONS: PK regulates circulating cholesterol levels through binding to LDLR and inducing its lysosomal degradation. Ablation of PK stabilizes LDLR, decreases LDL cholesterol, and prevents atherosclerotic plaque development. This study suggests that PK is a promising therapeutic target to treat atherosclerotic cardiovascular disease.


Subject(s)
Atherosclerosis/metabolism , Atherosclerosis/prevention & control , Cholesterol, LDL/metabolism , Plaque, Atherosclerotic/metabolism , Plaque, Atherosclerotic/prevention & control , Prekallikrein/deficiency , Receptors, LDL/metabolism , Animals , Atherosclerosis/genetics , Cholesterol, LDL/genetics , Lysosomes/genetics , Lysosomes/metabolism , Mice , Mice, Knockout , Plaque, Atherosclerotic/genetics , Prekallikrein/metabolism , Proteolysis , Receptors, LDL/genetics
13.
Nat Commun ; 13(1): 478, 2022 01 25.
Article in English | MEDLINE | ID: mdl-35078991

ABSTRACT

N6-methyladenosine (m6A) plays important role in lineage specifications of embryonic stem cells. However, it is still difficult to systematically dissect the specific m6A sites that are essential for early lineage differentiation. Here, we develop an adenine base editor-based strategy to systematically identify functional m6A sites that control lineage decisions of human embryonic stem cells. We design 7999 sgRNAs targeting 6048 m6A sites to screen for m6A sites that act as either boosters or barriers to definitive endoderm specification of human embryonic stem cells. We identify 78 sgRNAs enriched in the non-definitive endoderm cells and 137 sgRNAs enriched in the definitive endoderm cells. We successfully validate two definitive endoderm promoting m6A sites on SOX2 and SDHAF1 as well as a definitive endoderm inhibiting m6A site on ADM. Our study provides a functional screening of m6A sites and paves the way for functional studies of m6A at individual m6A site level.


Subject(s)
Adenosine/analogs & derivatives , Cell Differentiation , Cell Lineage , Endoderm/cytology , Gene Expression Regulation, Developmental , Human Embryonic Stem Cells/metabolism , SOXB1 Transcription Factors/metabolism , Adenosine/genetics , Adenosine/metabolism , Adrenomedullin/genetics , Adrenomedullin/metabolism , CRISPR-Cas Systems/genetics , Cells, Cultured , Endoderm/metabolism , Humans , Proteins/genetics , Proteins/metabolism , SOXB1 Transcription Factors/genetics
14.
Plant Dis ; 106(2): 741-744, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34598657

ABSTRACT

Xanthomonas oryzae pv. oryzae is the causal agent of bacterial blight, one of the most devastating diseases of rice. Here, a hypervirulent strain, C9-3, defeating Xa1, Xa10, xa13, and Xa23 resistance genes, was used to extract genomic DNA for single molecule real-time (SMRT) sequencing. After assembly, the genome consists of a single-circular chromosome with the size of 4,924,298 bp with G+C content of 63.7% and contains 4,715 genes. Annotation and analysis of the TALE genes using a suite of applications named AnnoTALE suggested that 17 transcription activator-like effectors, including 15 typical TALEs and 2 iTALEs/truncTALEs, were encoded in the genome. The approach and genome resource will contribute to the discovery of new virulence effectors and understanding on rice-X. oryzae pv. oryzae interactions.


Subject(s)
Oryza , Xanthomonas , Oryza/microbiology , Plant Diseases/microbiology , Plant Proteins/genetics , Xanthomonas/genetics
15.
Front Cardiovasc Med ; 8: 766613, 2021.
Article in English | MEDLINE | ID: mdl-34938784

ABSTRACT

Background: Vascular calcification (VC) is an important predictor of prognosis in atherosclerosis, the phenotypic transformation of vascular smooth muscle cells (VSMCs) is thought to be a process of VC. However, the implications and potential mechanisms for VSMCs phenotypic transition remain unknown. Methods: To study the transformation of vascular smooth muscle cells (VSMCs) in the calcification early period, we analyzed single-cell sequencing data from carotid artery calcified core and paracellular tissue, based on the results of enrichment analysis and protein-protein interaction analysis. Upstream transcription factors were tracked and finally the results were validated using the MESA database. Results: We successfully identified a subpopulation of inflammatory macrophage-like VSMCs and determined that MMP9 is an important factor in the phenotypic transformation of VSMCs. We found that RELA regulates MMP9 expression and that knockdown of RELA attenuated MMP9 expression and reduced the expression of BMP2 and the macrophage marker LGALS3 in vascular smooth muscle in inflammatory states, while serum levels of MMP9 correlated significantly with the inflammatory response. Conclusion: This study reveals that the phenotypic transformation of VSMCs can be regulated by modulating MMP9, providing a new idea for the early treatment of VC.

16.
Article in English | MEDLINE | ID: mdl-34954129

ABSTRACT

Serine/arginine-rich splicing factor 7 (SRSF7), a known splicing factor, has been revealed to play oncogenic roles in multiple cancers. However, the mechanisms underlying its oncogenic roles have not been well addressed. Here, based on N6-methyladenosine (m6A) co-methylation network analysis across diverse cell lines, we find that the gene expression of SRSF7 is positively correlated with glioblastoma (GBM) cell-specific m6A methylation. We then indicate that SRSF7 is a novel m6A regulator, which specifically facilitates the m6A methylation near its binding sites on the mRNAs involved in cell proliferation and migration, through recruiting the methyltransferase complex. Moreover, SRSF7 promotes the proliferation and migration of GBM cells largely dependent on the presence of the m6A methyltransferase. The two m6A sites on PDZ-binding kinase (PBK) are regulated by SRSF7 and partially mediate the effects of SRSF7 in GBM cells through recognition by insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). Together, our discovery reveals a novel role of SRSF7 in regulating m6A and validates the presence and functional importance of temporal- and spatial-specific regulation of m6A mediated by RNA-binding proteins (RBPs).

17.
Biochim Biophys Acta Mol Cell Biol Lipids ; 1866(11): 159006, 2021 11.
Article in English | MEDLINE | ID: mdl-34274505

ABSTRACT

Hypercholesterolemia has strong heritability and about 40-60% of hypercholesterolemia is caused by genetic risk factors. A number of monogenic genes have been identified so far for familial hypercholesterolemia (FH). However, in the general population, more than 90% of individuals with LDL cholesterol over 190 mg/dL do not carry known FH mutations. Large scale whole-exome sequencing has identified thousands of variants that are predicted to be loss-of-function (LoF) and each individual has a median of about twenty rare LoF variants and several hundreds more common LoF variants. However, majority of those variants have not been characterized and their functional consequence remains largely unknown. Rs77542162 is a common missense variant in ABCA6 and is strongly associated with hypercholesterolemia in different populations. ABCA6 is a cholesterol responsive gene and has been suggested to play a role in lipid metabolism. However, whether and how rs77542162 and ABCA6 regulate lipoprotein metabolism remain unknown. In current study, we systemically characterized the function of rs77542162 and ABCA6 in cultured cells and in vivo of rodents. We found that Abca6 is specifically expressed on the basolateral surface of hepatocytes in mouse liver. The rs77542162 variant disrupts ABCA6 protein stability and results in loss of functional protein. However, we found no evidence that Abca6 plays a role in lipoprotein metabolism in either normal mice or hypercholesterolemia mice or hamsters. Thus, our results suggest that Abca6 does not regulate lipoprotein metabolism in rodents and highlight the challenge and importance of functional characterization of disease-associated variants in animal models.


Subject(s)
ATP-Binding Cassette Transporters/metabolism , Hypercholesterolemia/genetics , Animals , Cells, Cultured , Cricetinae , HEK293 Cells , Humans , Hypercholesterolemia/metabolism , Lipoproteins/metabolism , Mice , Mice, Inbred C57BL , Risk Factors
18.
Genome Biol ; 22(1): 180, 2021 06 13.
Article in English | MEDLINE | ID: mdl-34120636

ABSTRACT

BACKGROUND: Canonical nonsense-mediated decay (NMD) is an important splicing-dependent process for mRNA surveillance in mammals. However, processed pseudogenes are not able to trigger NMD due to their lack of introns. It is largely unknown whether they have evolved other surveillance mechanisms. RESULTS: Here, we find that the RNAs of pseudogenes, especially processed pseudogenes, have dramatically higher m6A levels than their cognate protein-coding genes, associated with de novo m6A peaks and motifs in human cells. Furthermore, pseudogenes have rapidly accumulated m6A motifs during evolution. The m6A sites of pseudogenes are evolutionarily younger than neutral sites and their m6A levels are increasing, supporting the idea that m6A on the RNAs of pseudogenes is under positive selection. We then find that the m6A RNA modification of processed, rather than unprocessed, pseudogenes promotes cytosolic RNA degradation and attenuates interference with the RNAs of their cognate protein-coding genes. We experimentally validate the m6A RNA modification of two processed pseudogenes, DSTNP2 and NAP1L4P1, which promotes the RNA degradation of both pseudogenes and their cognate protein-coding genes DSTN and NAP1L4. In addition, the m6A of DSTNP2 regulation of DSTN is partially dependent on the miRNA miR-362-5p. CONCLUSIONS: Our discovery reveals a novel evolutionary role of m6A RNA modification in cleaning up the unnecessary processed pseudogene transcripts to attenuate their interference with the regulatory network of protein-coding genes.


Subject(s)
Adenosine/analogs & derivatives , Genome, Human , Pseudogenes , RNA Splicing , RNA, Messenger/genetics , Selection, Genetic , Adenosine/genetics , Adenosine/metabolism , Cell Line , Cell Line, Transformed , Destrin/genetics , Destrin/metabolism , HEK293 Cells , HapMap Project , Human Embryonic Stem Cells/cytology , Human Embryonic Stem Cells/metabolism , Humans , Lymphocytes/cytology , Lymphocytes/metabolism , MicroRNAs/genetics , MicroRNAs/metabolism , Nonsense Mediated mRNA Decay , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , RNA, Messenger/metabolism
19.
Brief Funct Genomics ; 20(4): 207-212, 2021 07 17.
Article in English | MEDLINE | ID: mdl-33615339

ABSTRACT

Post-transcriptional processing of RNAs plays important roles in a variety of physiological and pathological processes. These processes can be precisely controlled by a series of RNA binding proteins and cotranscriptionally regulated by transcription factors as well as histone modifications. With the rapid development of high-throughput sequencing techniques, multiomics data have been broadly used to study the mechanisms underlying the important biological processes. However, how to use these high-throughput sequencing data to elucidate the fundamental regulatory roles of post-transcriptional processes is still of great challenge. This review summarizes the regulatory mechanisms of post-transcriptional processes and the general principles and approaches to dissect these mechanisms by integrating multiomics data as well as public resources.


Subject(s)
RNA Processing, Post-Transcriptional , Transcriptome , High-Throughput Nucleotide Sequencing , RNA/metabolism , Sequence Analysis, RNA , Transcriptome/genetics
20.
EMBO Rep ; 22(4): e50128, 2021 04 07.
Article in English | MEDLINE | ID: mdl-33605073

ABSTRACT

N6 -methyladenosine (m6 A) modification of mRNA mediates diverse cellular and viral functions. Infection with Epstein-Barr virus (EBV) is causally associated with nasopharyngeal carcinoma (NPC), 10% of gastric carcinoma, and various B-cell lymphomas, in which the viral latent and lytic phases both play vital roles. Here, we show that EBV transcripts exhibit differential m6 A modification in human NPC biopsies, patient-derived xenograft tissues, and cells at different EBV infection stages. m6 A-modified EBV transcripts are recognized and destabilized by the YTHDF1 protein, which leads to the m6 A-dependent suppression of EBV infection and replication. Mechanistically, YTHDF1 hastens viral RNA decapping and mediates RNA decay by recruiting RNA degradation complexes, including ZAP, DDX17, and DCP2, thereby post-transcriptionally downregulating the expression of EBV genes. Taken together, our results reveal the critical roles of m6 A modifications and their reader YTHDF1 in EBV replication. These findings contribute novel targets for the treatment of EBV-associated cancers.


Subject(s)
Epstein-Barr Virus Infections , Nasopharyngeal Neoplasms , Adenosine/analogs & derivatives , Carrier Proteins , Herpesvirus 4, Human/genetics , Humans , RNA Stability , RNA-Binding Proteins/genetics , Virus Replication
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