Publications by authors named "Shan Ge"

60 Publications

[Effect of swertiamarin, gentiopicrin and sweroside on cell apoptosis and expression of Bcl-2 in rheumatoid arthritis fibroblast-like synoviocytes].

Zhongguo Zhong Yao Za Zhi 2021 Jan;46(2):406-411

School of Pharmacy, Gansu University of Chinese Medicine Lanzhou 730000, China.

The aim of this paper was to discuss the effect of swertiamarin, gentiopicrin and sweroside on rheumatoid arthritis fibroblast-like synoviocytes(RA-FLSs) and B-cell lymphoma-2(Bcl-2) and their mechanisms. ZINC database and RCSB PDB database were retrieved for 3 D chemical structures of swertiamarin, gentiopicrin and sweroside and 3 D target protein structures. AutoDock Mgltools 1.5.6, AutoDockVina 1.1.2 and pyMOL 2.2.0 were applied for molecular docking to analyze the relationship between Bcl-2(1 GJH) target protein and important ingredients. The cell apoptosis of RA-FLSs was tested by Annexin V-FITC. The Bcl-2 protein expression of RA-FLSs treated with different ingredients was tested by Western blot. The Bcl-2 mRNA expression of RA-FLSs treated with different ingredients was tested by RT-PCR. Swertiamarin, gentiopicrin and sweroside were docked well with Bcl-2(1 GJH). The binding energy of swertiamarin was-6.9 kcal·mol~(-1), the binding energy of gentiopicrin was-6.7 kcal·mol~(-1) and the binding energy of sweroside was-6.4 kcal·mol~(-1). Compared with the blank group, the Bcl-2 protein expression of each group were reduced, while that of the gentiopicrin group was the highest(P<0.01). Compared with the blank group, the Bcl-2 mRNA expression of each groups were reduced. Gentiopicrin can reduce the Bcl-2 protein expression and the Bcl-2 mRNA expression, so as to promote the RA-FLSs apoptosis.
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http://dx.doi.org/10.19540/j.cnki.cjcmm.20200927.401DOI Listing
January 2021

CircRNA in cancer: Fundamental mechanism and clinical potential.

Authors:
Liang Chen Ge Shan

Cancer Lett 2021 May 18;505:49-57. Epub 2021 Feb 18.

Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China. Electronic address:

Circular RNAs (CircRNAs) are a class of single-stranded noncoding RNAs that are formed in a circular conformation via non-canonical splicing or back-splicing events. Aberrant expressions of many circRNAs are observed in diverse cancers, indicating their crucial roles in tumorigenesis and tumor development. Recently, several pieces of evidence have revealed that many circRNAs are involved in the promotion or suppression of cancers to varying degrees via different molecular mechanisms. Here in this review, we present a summary of the characteristics, types, biogenesis, and functions of circRNAs, and outline a series of the most recently studied circRNAs and their functional mechanisms in multiple cancer types with future perspectives. With great advances in nucleic acid-based therapeutic tools, circRNAs could be further explored as targetable molecules in future cancer treatments.0.
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http://dx.doi.org/10.1016/j.canlet.2021.02.004DOI Listing
May 2021

Identification and detection of mecciRNAs.

Methods 2021 Feb 13. Epub 2021 Feb 13.

Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, CAS, Shanghai 200031, China. Electronic address:

Mitochondria participate in series of metabolic processes and cellular events. It is widely known that only 13 proteins are encoded by the mammalian mitochondria genome. However, it is not acknowledged until recently that mitochondrial genomes encode hundreds of circular RNAs, named as mecciRNAs. Some of these mecciRNAs can serve as molecular chaperones to help folding nuclear-encoded proteins and facilitating their mitochondrial entrance. As a novel type of circular RNAs, functions and characteristics of mecciRNAs are waiting for further exploration and methods for mecciRNA studies need to be improved. Here, we describe detailed methods for mitochondrial RNA isolation and mecciRNA detection. In addition, we present effective mecciRNA overexpression and knockdown strategies for future functional studies of mecciRNAs.
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http://dx.doi.org/10.1016/j.ymeth.2021.02.006DOI Listing
February 2021

Repurposing bortezomib for choroidal neovascularization treatment via antagonizing VEGF-A and PDGF-D mediated signaling.

Exp Eye Res 2021 Mar 18;204:108446. Epub 2021 Jan 18.

School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, PR China; State Key Laboratory of Optometry, Ophthalmology, and Visual Science, 270 Xueyuan Road, Wenzhou, Zhejiang, 325003, PR China. Electronic address:

Neovascular age-related macular degeneration (neoAMD) is the leading cause of blindness in AMD and manifests as choroidal neovascularization (CNV). Anti-vascular endothelial growth factor (VEGF) therapies are the mainstay treatments but with limited efficacy and cause detrimental effects on the retina after long-term application. These disadvantages warrant alternative strategy. Herein, we examined the effect on CNV by intravitreal injection of bortezomib, a reversible proteasome inhibitor, and further dissected the mechanism. Krypton red Laser was used to create CNV model in mice. The angiogenesis volume was assessed in choroidal flat-mount with isolectin GS-IB4 labeling and the leakage was examined with fluorescein fundus angiography. Injection of Bor inhibited angiogenesis in the CNV model which was dose-dependent; the injection significantly inhibited leakage as well. Furthermore, Bor injection reduced the contents of VEGF-A, macrophage chemotactic factor 1 (MCP-1), and platelet-derived growth factor (PDGF)-D but not PDGF-B, examined by enzyme-linked immunosorbent assay, in choroid/retinal pigment epithelium (RPE) tissue. These injections also reduced phospho-VEGFR-2 and phospho-PDGFRβ in choroid/RPE tissue examined by immunoblotting. Moreover, Bor inhibited the recruitment of mural cells or macrophages to laser-injured spots. Injection of Bor indicated negative effect on scotopic and photopic responses recorded by electroretinogram. Altogether, intravitreal injection of Bor significantly reduced CNV by antagonizing VEGF-A/Flk-1 and PDGF-D/PDGFRβ pathways without impacting electroretinography parameters. Thus, Bor may offer an invaluable therapy for the prevention and treatment of neoAMD.
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http://dx.doi.org/10.1016/j.exer.2021.108446DOI Listing
March 2021

Circular RNAs from play conserved roles in protection against stress-induced fertility decline.

Sci Adv 2020 Nov 11;6(46). Epub 2020 Nov 11.

Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.

Circular RNAs (circRNAs) are a large family of newly identified transcripts, and their physiological roles and evolutionary significance require further characterization. Here, we identify circRNAs generated from a conserved reproductive gene, , in species from to humans. Flies missing circular (circBoule) RNAs display decreased male fertility, and sperm of circBoule knockout mice exhibit decreased fertilization capacity, when under heat stress conditions. During spermatogenesis, fly circBoule RNAs interact with heat shock proteins (HSPs) Hsc4 and Hsp60C, and mouse circBoule RNAs in sperm interact with HSPA2. circBoule RNAs regulate levels of HSPs by promoting their ubiquitination. The interaction between HSPA2 and circBoule RNAs is conserved in human sperm, and lower levels of the human circBoule RNAs circEx3-6 and circEx2-7 are found in asthenozoospermic sperm. Our findings reveal conserved physiological functions of circBoule RNAs in metazoans and suggest that specific circRNAs may be critical modulators of male reproductive function against stresses in animals.
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http://dx.doi.org/10.1126/sciadv.abb7426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7673749PMC
November 2020

Vision function of pseudophakic eyes with posterior capsular opacification under different speed and spatial frequency.

Int Ophthalmol 2020 Dec 8;40(12):3491-3500. Epub 2020 Oct 8.

Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, 49 North Garden Road, Haidian District, Beijing, 100191, China.

Purpose: To investigate the characteristics of dynamic visual acuity (DVA) and contrast sensitivity (CS) in pseudophakic patients with posterior capsular opacification (PCO).

Methods: Fifty-four eyes (36 patients) with PCO planned for laser capsulotomy were recruited. They underwent examinations of static visual acuity (SVA), DVA, CS and optical quality analysis (OQAS) before and one week after the laser treatment. Improvements in each index after laser treatment were analyzed. The visual quality of patients with good initial vision was studied separately.

Results: SVA, DVA and CS all significantly increased after capsulotomy (P < 0.05). Postoperative improvements in DVA were higher than in SVA, but they decreased when the speed increased. DVA at 15 dps gained the most improvement after capsulotomy. DVA at all analyzed speeds was significantly lower than SVA (P = 0.000). There was a significant speed-dependent decrease in DVA at lower speeds compared with higher speeds. The postoperative improvements in CS decreased when the spatial frequency was increased. The CS at the lower frequencies of 3 cpd and 6 cpd was the most improved after capsulotomy. CS was much lower at high frequencies (p < 0.05). There was a significant decrease in CS at higher spatial frequencies compared with lower frequencies. DVA improvements were correlated with CS improvements at medium spatial frequencies and with objective scattering index and Strehl ratio. The CS at all frequencies significantly improved for patients with good initial vision.

Conclusion: PCO could impair dynamic vision function, but CS was a more sensitive indication of visual complaints in patients with slight PCO.
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http://dx.doi.org/10.1007/s10792-020-01536-9DOI Listing
December 2020

The physiological function of long-noncoding RNAs.

Authors:
He Chen Ge Shan

Noncoding RNA Res 2020 Dec 17;5(4):178-184. Epub 2020 Sep 17.

CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, 230027, China.

The physiological processes of cells and organisms are regulated by various biological macromolecules, including long-noncoding RNAs (lncRNAs), which cannot be translated into protein and are different from small-noncoding RNAs on their length. In animals, lncRNAs are involved in development, metabolism, reproduction, aging and other life events by or effects. For many functional lncRNAs, there is growing evidence that they play different roles on cellular level and organismal level. On the other hand, many annotated lncRNAs are not essential and could be transcription noises. In this minireview, we investigate the physiological function of lncRNAs in cells and focus on their functions and functional mechanisms on the organismal level. The studies on lncRNAs using different classic animal models such as worms and flies are summarized and discussed in this article.
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http://dx.doi.org/10.1016/j.ncrna.2020.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7494506PMC
December 2020

Editorial: Non-Coding RNAs and Human Diseases.

Front Genet 2020 25;11:523. Epub 2020 May 25.

Department of Human Genetics, Emory University, Atlanta, GA, United States.

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http://dx.doi.org/10.3389/fgene.2020.00523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7262963PMC
May 2020

U1 snRNP regulates chromatin retention of noncoding RNAs.

Nature 2020 04 11;580(7801):147-150. Epub 2020 Mar 11.

Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China.

Long noncoding RNAs (lncRNAs) and promoter- or enhancer-associated unstable transcripts locate preferentially to chromatin, where some regulate chromatin structure, transcription and RNA processing. Although several RNA sequences responsible for nuclear localization have been identified-such as repeats in the lncRNA Xist and Alu-like elements in long RNAs-how lncRNAs as a class are enriched at chromatin remains unknown. Here we describe a random, mutagenesis-coupled, high-throughput method that we name 'RNA elements for subcellular localization by sequencing' (mutREL-seq). Using this method, we discovered an RNA motif that recognizes the U1 small nuclear ribonucleoprotein (snRNP) and is essential for the localization of reporter RNAs to chromatin. Across the genome, chromatin-bound lncRNAs are enriched with 5' splice sites and depleted of 3' splice sites, and exhibit high levels of U1 snRNA binding compared with cytoplasm-localized messenger RNAs. Acute depletion of U1 snRNA or of the U1 snRNP protein component SNRNP70 markedly reduces the chromatin association of hundreds of lncRNAs and unstable transcripts, without altering the overall transcription rate in cells. In addition, rapid degradation of SNRNP70 reduces the localization of both nascent and polyadenylated lncRNA transcripts to chromatin, and disrupts the nuclear and genome-wide localization of the lncRNA Malat1. Moreover, U1 snRNP interacts with transcriptionally engaged RNA polymerase II. These results show that U1 snRNP acts widely to tether and mobilize lncRNAs to chromatin in a transcription-dependent manner. Our findings have uncovered a previously unknown role of U1 snRNP beyond the processing of precursor mRNA, and provide molecular insight into how lncRNAs are recruited to regulatory sites to carry out chromatin-associated functions.
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http://dx.doi.org/10.1038/s41586-020-2105-3DOI Listing
April 2020

Identification of mecciRNAs and their roles in the mitochondrial entry of proteins.

Sci China Life Sci 2020 10 21;63(10):1429-1449. Epub 2020 Jan 21.

Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China.

Mammalian mitochondria have small genomes encoding very limited numbers of proteins. Over one thousand proteins and noncoding RNAs encoded by the nuclear genome must be imported from the cytosol into the mitochondria. Here, we report the identification of hundreds of circular RNAs (mecciRNAs) encoded by the mitochondrial genome. We provide both in vitro and in vivo evidence to show that mecciRNAs facilitate the mitochondrial entry of nuclear-encoded proteins by serving as molecular chaperones in the folding of imported proteins. Known components involved in mitochondrial protein and RNA importation, such as TOM40 and PNPASE, interact with mecciRNAs and regulate protein entry. The expression of mecciRNAs is regulated, and these transcripts are critical for the adaption of mitochondria to physiological conditions and diseases such as stresses and cancers by modulating mitochondrial protein importation. mecciRNAs and their associated physiological roles add categories and functions to the known eukaryotic circular RNAs and shed novel light on the communication between mitochondria and the nucleus.
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http://dx.doi.org/10.1007/s11427-020-1631-9DOI Listing
October 2020

Defining an evolutionarily conserved role of GW182 in circular RNA degradation.

Cell Discov 2019 17;5:45. Epub 2019 Sep 17.

1School of Life Sciences, Chongqing University, Chongqing, 401331 China.

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http://dx.doi.org/10.1038/s41421-019-0113-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796862PMC
September 2019

ΔNp63α exerts antitumor functions in cervical squamous cell carcinoma.

Oncogene 2020 01 1;39(4):905-921. Epub 2019 Oct 1.

Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science & Technology of China, Anhui Provincial Hospital, Hefei, 230001, Anhui Province, China.

The molecular basis underlying the aggressive nature and excessive proliferation of cervical squamous cancer cell remains unclear. ΔNp63α is the predominant isotype of p63 expressed in the epithelia and regulates epithelial cell differentiation. The pro-/anti-tumor role of ΔNp63α in different kinds of solid tumors remains controversial and the precise molecular mechanisms are still elusive. In this study, we uncovered the molecular functions of ΔNp63α in cervical squamous cell carcinoma to clarify its roles as a tumor suppressor. We demonstrated that ΔNp63α suppressed cell migration, invasiveness, and tumor growth in SiHa and ME-180 cells with both in vivo and in vitro assays. Mechanistic investigation via RNA-sequencing and chromatin immunoprecipitation-sequencing revealed that ΔNp63α exerted its antitumor capacity via regulating the expression of a cohort of cell junction genes. Further, we showed that ZNF385B and CLDN1 were two direct ΔNp63α targets with significant relevance to cervical squamous cell carcinoma examined in cell cultures, tumor xenografts, and clinic tumors. We also demonstrated that ΔNp63α downregulated NFATC1 to reduce cisplatin resistance. These findings shed new lights on functions of ΔNp63α in tumors and providing novel insights in targeted therapy of cervical cancers.
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http://dx.doi.org/10.1038/s41388-019-1033-xDOI Listing
January 2020

Long noncoding RNA EMS connects c-Myc to cell cycle control and tumorigenesis.

Proc Natl Acad Sci U S A 2019 07 1;116(29):14620-14629. Epub 2019 Jul 1.

Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, First Affiliated Hospital of University of Science and Technology of China, School of Life Sciences, University of Science and Technology of China (USTC), 230027 Hefei, Anhui, China;

Deregulated expression of c-Myc is an important molecular hallmark of cancer. The oncogenic function of c-Myc has been largely attributed to its intrinsic nature as a master transcription factor. Here, we report the long noncoding RNA (lncRNA) E2F1 messenger RNA (mRNA) stabilizing factor (EMS) as a direct c-Myc transcriptional target. EMS functions as an oncogenic molecule by promoting G1/S cell cycle progression. Mechanistically, EMS cooperates with the RNA binding protein RALY to stabilize E2F1 mRNA, and thereby increases E2F1 expression. Furthermore, EMS is able to connect c-Myc to cell cycle control and tumorigenesis via modulating E2F1 mRNA stability. Together, these findings reveal a previously unappreciated mechanism through which c-Myc induces E2F1 expression and also implicate EMS as an important player in the regulation of c-Myc function.
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http://dx.doi.org/10.1073/pnas.1903432116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642410PMC
July 2019

Analyses of a Panel of Transcripts Identified From a Small Sample Size and Construction of RNA Networks in Hepatocellular Carcinoma.

Front Genet 2019 8;10:431. Epub 2019 May 8.

Hefei National Laboratory for Physical Sciences at Microscale, The Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China.

Hepatocellular carcinoma (HCC) is one of the most common cancers in the world. Dysregulation of mRNAs and non-coding RNAs (ncRNAs) plays critical roles in the progression of HCC. Here, we investigated HCC samples by RNA-seq and identified a series of dysregulated RNAs in HCC. Various bioinformatics analyses established long non-coding RNA (lncRNA)-mRNA co-expression and competing endogenous RNA (ceRNA) networks in circRNA-miRNA-mRNA axis, indicating the potential and/or regulatory roles of lncRNAs and circRNAs. Moreover, GO pathway analysis showed that these identified RNAs were associated with many biological processes that were related to tumorigenesis and tumor progression. In conclusion, we systematically established functional networks of lncRNA-mRNA, circRNA-miRNA-mRNA to further unveil the potential interactions and biological processes in HCC. These results provide further insights into gene expression network of HCC and may assist future diagnosis of HCC.
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http://dx.doi.org/10.3389/fgene.2019.00431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6530380PMC
May 2019

Effects of LncRNA Lnc-LIF-AS on cell proliferation, migration and invasion in a human cervical cancer cell line.

Cytokine 2019 08 11;120:165-175. Epub 2019 May 11.

Department of Obstetrics and Gynecology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei 230001, China. Electronic address:

This study explored the effect of LncRNA Lnc-LIF-AS on cell proliferation, migration and invasion in the human cervical cancer (HCC) cell line SiHa. SiHa cells had the lowest expression of Lnc-LIF-AS in the 4 human cervical cancer cell lines (SiHa, ME-180, C-33A and HeLa) and were transfected and divided into the SiHa/con (transfected with pMIGRI) cell group, SiHa/Lnc-LIF-AS (transfected with pMIGRI-Lnc-LIF-AS) cell group, and SiHa/Lnc-LIF-AS-DN (transfected with pMIGRI-Lnc-LIF-AS-DN, in which the sequences overlapping with LIF mRNA was deleted) cell group. Overexpression of Lnc-LIF-AS could promote the proliferation, colony formation, invasion and migration in SiHa and ME-180 cells. And the low expression of Lnc-LIF-AS suppress the proliferation, colony formation invasion and migration in HeLa cells when the Lnc-LIF-AS expression has been suppressed. In the SiHa/Lnc-LIF-AS cells group, the cell cycle was mainly halted in the S phase and overexpression of Lnc-LIF-AS had no effect on the apoptosis of SiHa cells. Overexpression of Lnc-LIF-AS could promote the secretion of LIF in SiHa cells, and the supernatant from SiHa/Lnc-LIF-AS cells could promote cell proliferation in the SiHa/con cells. The STAT3 inhibitor could inhibit cell proliferation in the SiHa/Lnc-LIF-AS cells. The expression level of Lnc-LIF-AS in cervical cancer tissues was higher than that in normal tissues and the expression level of Lnc-LIF-AS was positively correlated with the level of LIF. In the SiHa/con and SiHa/Lnc-LIF-AS-DN cell groups, there were no significant differences in cell proliferation, cell migration and cell invasion. The overexpression of Lnc-LIF-AS can promote cell proliferation, migration and invasion in cervical cancer cells, and the core function domain of this lncRNA was located in the overlapping a 3'-UTR base sequence of LIF mRNA.
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http://dx.doi.org/10.1016/j.cyto.2019.05.004DOI Listing
August 2019

Intravenous injection of l-aspartic acid β-hydroxamate attenuates choroidal neovascularization via anti-VEGF and anti-inflammation.

Exp Eye Res 2019 05 24;182:93-100. Epub 2019 Mar 24.

School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, China; State Key Laboratory of Optometry, Ophthalmology, and Visual Science, Wenzhou, Zhejiang, 325027, China. Electronic address:

Choroidal neovascularization (CNV) is a hallmark of exudative age-related macular degeneration (exAMD) and a major cause of visual loss in AMD. Despite the widespread use of anti-VEGF therapy, serious adverse effects arise from repeated intravitreal injection of anti-VEGF antibodies, which warrant alternative strategy. We report herein that in a CNV murine model created by krypton red laser, intravenous injection of a serine racemase inhibitor, l-Aspartic acid β-hydroxamate (L-ABH), significantly reduced CNV at the dose 6 mg/kg on the first day before and followed by 3 mg/kg on the third day after laser injury. The CNV volumes were analyzed with isolectin GS-IB4 staining on choroidal/RPE flat mounts on the seventh day after laser injury. Injection of L-ABH did not produce negative effects on retinal function and visual behavior. To dissect the mechanism in vitro, pretreatment with L-ABH in primary RPE cultures significantly reduced production of vascular endothelial growth factor (VEGF) and macrophage chemotactic protein 1 (MCP-1) by TNFα-primed RPEs. Consistent with these observations, L-ABH pretreatment significantly attenuated macrophage migration mediated by TNFα-primed RPE. Collectively, intravenous injection of L-ABH significantly reduced CNV volumes via reducing production of VEGF and MCP-1 by inflammation-primed RPEs.
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http://dx.doi.org/10.1016/j.exer.2019.03.018DOI Listing
May 2019

Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants.

Genome Biol 2019 01 8;20(1). Epub 2019 Jan 8.

Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.

Background: Long intergenic RNAs (lincRNAs) play critical roles in eukaryotic cells, but systematic analyses of the lincRNAs of an animal for phenotypes are lacking. We generate CRISPR knockout strains for Caenorhabditis elegans lincRNAs and evaluate their phenotypes.

Results: C. elegans lincRNAs demonstrate global features such as shorter length and fewer exons than mRNAs. For the systematic evaluation of C. elegans lincRNAs, we produce CRISPR knockout strains for 155 of the total 170 C. elegans lincRNAs. Mutants of 23 lincRNAs show phenotypes in 6 analyzed traits. We investigate these lincRNAs by phenotype for their gene expression patterns and potential functional mechanisms. Some C. elegans lincRNAs play cis roles to modulate the expression of their neighboring genes, and several lincRNAs play trans roles as ceRNAs against microRNAs. We also examine the regulation of lincRNA expression by transcription factors, and we dissect the pathway by which two transcription factors, UNC-30 and UNC-55, together control the expression of linc-73. Furthermore, linc-73 possesses a cis function to modulate the expression of its neighboring kinesin gene unc-104 and thus plays roles in C. elegans locomotion.

Conclusions: By using CRISPR/cas9 technology, we generate knockout strains of 155 C. elegans lincRNAs as valuable resources for studies in noncoding RNAs, and we provide biological insights for 23 lincRNAs with the phenotypes identified in this study.
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http://dx.doi.org/10.1186/s13059-018-1619-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325887PMC
January 2019

Loss of miR-83 extends lifespan and affects target gene expression in an age-dependent manner in Caenorhabditis elegans.

J Genet Genomics 2018 12 9;45(12):651-662. Epub 2018 Dec 9.

Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Centre for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. Electronic address:

MicroRNAs (miRNAs) are short non-coding RNAs that are involved in the post-transcriptional regulation of protein-coding genes. miRNAs modulate lifespan and the aging process in a variety of organisms. In this study, we identified a role of miR-83 in regulating lifespan of Caenorhabditis elegans. mir-83 mutants exhibited extended lifespan, and the overexpression of miR-83 was sufficient to decrease the prolonged lifespan of the mutants. We observed upregulation of the expression levels of a set of miR-83 target genes in young mir-83 mutant adults; while different sets of genes were upregulated in older mir-83 mutant adults. In vivo assays showed that miR-83 regulated expression of target genes including din-1, spp-9 and col-178, and we demonstrated that daf-16 and din-1 were required for the extension of lifespan in the mir-83 mutants. The regulation of din-1 by miR-83 during aging resulted in the differential expression of din-1 targets such as gst-4 and gst-10. In daf-2 mutants, the expression level of miR-83 was significantly reduced compared to wild-type animals. We identified a role for miR-83 in modulating lifespan in C. elegans and provided molecular insights into its functional mechanism.
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http://dx.doi.org/10.1016/j.jgg.2018.11.003DOI Listing
December 2018

Roles of genetic and microenvironmental factors in cancer epithelial-to-mesenchymal transition and therapeutic implication.

Exp Cell Res 2018 09 31;370(2):190-197. Epub 2018 Jul 31.

Department of Immunology, Basic Medical School, Guizhou Medical University, Guiyang 550004, China.

Epithelial-to-mesenchymal transition (EMT) is a process in which epithelial cells lose their cell-cell contacts resulting in the formation of mesenchymal cells with migratory properties. Increasing evidence indicate EMT plays a key role in the invasion, metastasis and therapeutic resistance of cancer and maintenance of the phenotype of cancer stem cells (CSCs), which makes the prognosis of patients worse. The progression of cancer from epithelial tissue towards a malignant phenotype is driven by multiple factors that remodel the tissue architecture. This review summarizes and analyzes current studies of genetic and microenvironmental factors in inducing and maintaining cancer EMT and therapeutic implications. This will enable a better understanding of the contribution of EMT-associated factors to cancer progression and highlights that genetic factors and tumor microenvironment responsible for EMT could be used as attractive targets for therapeutic intervention.
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http://dx.doi.org/10.1016/j.yexcr.2018.07.046DOI Listing
September 2018

[Long-term effects of neonatal exposure to bisphenol A on testes structure and the expression of Boule in testes of male mice].

Wei Sheng Yan Jiu 2017 Nov;46(6):975-980

School of Biological Science and Technology, Weifang Medical University, Weifang 261053, China.

Objective: To investigate the long-term effects and the mechanism of neonatal bisphenol A( BPA) exposure on mouse testicular structure and Boule expression.

Methods: A total of 12 pregnant ICR mice were randomly divided into three groups:blank control group, negative control group( corn oil) and BPA 100 μg/kg group. After delivery, BPA was given daily by neck subcutaneous injection to the offspring male mice from postnatal day( PND 1) to PND 21. The offspring male mice were sacrificed on PND35 and PND 70. Morphological changes of testes were detected with hematoxylin-eosin staining, the level of Boule mRNA expression was determined by RT-PCR, the expression of Boule protein was detected by immunofluorescence and Western blotting.

Results: Compared with blank control group and negative control group, the diameter and the epithelium thickness of seminiferous epithelium in the same period( PND 35, PND 70)were significantly decreased and the lumen was significantly increased( P < 0. 05) in the testes of BPA( 100 μg/kg) group. In addition, the expressions of Boule mRNA and protein were decreased remarkably( P < 0. 05, P < 0. 01) in testes of BPA 100 μg/kg group.

Conclusion: Neonatal BPA exposure has a long-term effect on mouse testicular development and may affect testicular development by decreasing the expression of Boule mRNA and protein in testes.
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November 2017

Targetable long non-coding RNAs in cancer treatments.

Cancer Lett 2018 04 16;418:119-124. Epub 2018 Jan 16.

CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China. Electronic address:

Aberrant expression of many long non-coding RNAs has been observed in various types of cancer, implicating their crucial roles in tumorigenesis and cancer progression. Emerging knowledge with regard to the critical physiological and pathological roles of long non-coding RNAs in cancers makes them potential targets in cancer treatments. In this review, we present a summary of the relatively well studied long non-coding RNAs that are involved in oncogenesis and outline their functions and functional mechanisms. Recent findings that may be utilized in therapeutic intervention are also highlighted. With the fast development in nucleic acid-based therapeutic reagents that can target disease associated RNAs, lncRNAs should be explored as potential targets in cancer treatments.
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http://dx.doi.org/10.1016/j.canlet.2018.01.042DOI Listing
April 2018

The DEAD-Box RNA Helicase DDX3 Interacts with mA RNA Demethylase ALKBH5.

Stem Cells Int 2017 23;2017:8596135. Epub 2017 Nov 23.

CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China.

DDX3 is a member of the family of DEAD-box RNA helicases. DDX3 is a multifaceted helicase and plays essential roles in key biological processes such as cell cycle, stress response, apoptosis, and RNA metabolism. In this study, we found that DDX3 interacted with ALKBH5, an mA RNA demethylase. The ATP domain of DDX3 and DSBH domain of ALKBH5 were indispensable to their interaction with each other. Furthermore, DDX3 could modulate the demethylation of mRNAs. We also showed that DDX3 regulated the methylation status of microRNAs and there was an interaction between DDX3 and AGO2. The dynamics of mA RNA modification is still a field demanding further investigation, and here, we add a link by showing that RNA demethylation can be regulated by proteins such as DDX3.
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http://dx.doi.org/10.1155/2017/8596135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5733242PMC
November 2017

Nonradioactive Northern Blot of circRNAs.

Methods Mol Biol 2018 ;1724:135-141

The CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, China.

Circular RNAs (circRNAs) are recognized as a special species of transcripts in metazoans with increasing studies, and northern blotting is a direct way to confirm the existence and to evaluate the size of individual circRNAs. Northern blotting probes can be radioactive isotope (P) labeled, which is not environment-friendly and sometimes inconvenient to use. Here, we describe a nonradioactive northern blot protocol with digoxigenin-labeled probe to detect circRNA.
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http://dx.doi.org/10.1007/978-1-4939-7562-4_11DOI Listing
January 2019

Convergent Transcriptional Programs Regulate cAMP Levels in C. elegans GABAergic Motor Neurons.

Dev Cell 2017 10 12;43(2):212-226.e7. Epub 2017 Oct 12.

CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China. Electronic address:

Both transcriptional regulation and signaling pathways play crucial roles in neuronal differentiation and plasticity. Caenorhabditis elegans possesses 19 GABAergic motor neurons (MNs) called D MNs, which are divided into two subgroups: DD and VD. DD, but not VD, MNs reverse their cellular polarity in a developmental process called respecification. UNC-30 and UNC-55 are two critical transcription factors in D MNs. By using chromatin immunoprecipitation with CRISPR/Cas9 knockin of GFP fusion, we uncovered the global targets of UNC-30 and UNC-55. UNC-30 and UNC-55 are largely converged to regulate over 1,300 noncoding and coding genes, and genes in multiple biological processes, including cAMP metabolism, are co-regulated. Increase in cAMP levels may serve as a timing signal for respecification, whereas UNC-55 regulates genes such as pde-4 to keep the cAMP levels low in VD. Other genes modulating DD respecification such as lin-14, irx-1, and oig-1 are also found to affect cAMP levels.
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http://dx.doi.org/10.1016/j.devcel.2017.09.013DOI Listing
October 2017

Comparing two approaches of miR-34a target identification, biotinylated-miRNA pulldown vs miRNA overexpression.

RNA Biol 2018 01 9;15(1):55-61. Epub 2017 Nov 9.

a CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences , University of Science and Technology of China , Hefei , China.

microRNAs (miRNAs) are critical regulators of gene expression. For elucidating functional roles of miRNAs, it is critical to identify their direct targets. There are debates about whether pulldown of biotinylated miRNA mimics can be used to identify miRNA targets or not. Here we show that biotin-labelled miR-34a can be loaded to AGO2, and AGO2 immunoprecipitation can pulldown biotinylated miR-34a (Bio-miR pulldown). RNA-sequencing (RNA-seq) of the Bio-miR pulldown RNAs efficiently identified miR-34a mRNA targets, which could be verified with luciferase assays. In contrast to the approach of Bio-miR pulldown, RNA-seq of miR-34a overexpression samples had limited value in identifying direct targets of miR-34a. It seems that pulldown of 3'-Biotin-tagged miRNA can identify bona fide microRNA targets at least for miR-34a.
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http://dx.doi.org/10.1080/15476286.2017.1391441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786020PMC
January 2018

Induction of miR-3648 Upon ER Stress and Its Regulatory Role in Cell Proliferation.

Int J Mol Sci 2017 Jun 29;18(7). Epub 2017 Jun 29.

Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.

MicroRNAs (miRNAs) play important roles under multiple cellular conditions including endoplasmic reticulum (ER) stress. We found that miR-3648, a human specific microRNA, was induced under ER stress. Moreover, Adenomatous polyposis coli 2 (APC2), a tumor suppressor and a negative regulator of Wnt signaling, was found to be the direct target of miR-3648. Levels of APC2 were downregulated when cells were under ER stress or after overexpressing miR-3648. Inhibition of miR-3648 by antagomir increased APC2 levels and decreased cell proliferation. Conversely, when miR-3648 was overexpressed, APC2 levels were decreased and the cell growth increased. Our data demonstrated that ER stress mediated induction of miR-3648 in human cells, which then downregulated APC2 to increase cell proliferation.
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http://dx.doi.org/10.3390/ijms18071375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5535868PMC
June 2017

Primate-specific Long Non-coding RNAs and MicroRNAs.

Genomics Proteomics Bioinformatics 2017 06 8;15(3):187-195. Epub 2017 Jun 8.

CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China. Electronic address:

Non-coding RNAs (ncRNAs) are critical regulators of gene expression in essentially all life forms. Long ncRNAs (lncRNAs) and microRNAs (miRNAs) are two important RNA classes possessing regulatory functions. Up to date, many primate-specific ncRNAs have been identified and investigated. Their expression specificity to primate lineage suggests primate-specific roles. It is thus critical to elucidate the biological significance of primate or even human-specific ncRNAs, and to develop potential ncRNA-based therapeutics. Here, we have summarized the studies regarding regulatory roles of some key primate-specific lncRNAs and miRNAs.
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http://dx.doi.org/10.1016/j.gpb.2017.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5487532PMC
June 2017

LncRNA expression profile of ΔNp63α in cervical squamous cancers and its suppressive effects on LIF expression.

Cytokine 2017 08 7;96:114-122. Epub 2017 Apr 7.

Department of Obstetrics and Gynecology, Anhui Provincial Hospital, Anhui Medical University, Hefei 230001, China. Electronic address:

We aim to determine the lncRNA targets of ΔNp63α in cervical cancer and molecular programs in cancerous differentiation. Different profiles of the lncRNAs were assayed and validated in overexpressing p63 SiHa cells (SiHa/ΔNp63α) and the control cell lines (SiHa/pCon). ENST00000422259, ENST00000447565 (Lnc-LIF-AS) and ENST00000469965, together with their related antisense mRNA DPYD (dihydropyrimidine dehydrogenase, a pyrimidine catabolic pathway gene), LIF (leukemia inhibitor factor) and FLNC (filamin C) were all notably differentially expressed in both ΔNp63α overexpression cells and knockdown cells. Here, we illustrated that ΔNp63α can inhibit the levels of LIF mRNA by direct transcription regulation and decrease LIF mRNA stability by suppressing the expression of Lnc-LIF-AS. An inverse interaction of LIF and ΔNp63α expression was as well validated in clinical samples of cervical cancer, and high level of LIF in cervical cancers was related with poor patient survival. The decrease of ΔNp63α also attenuated the differentiation of cervical cancerous cells. Suggesting that ΔNp63α may be form a complex network in regulation cervical cancerous differentiation.
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http://dx.doi.org/10.1016/j.cyto.2017.04.001DOI Listing
August 2017

The RNA-binding protein QKI5 regulates primary miR-124-1 processing via a distal RNA motif during erythropoiesis.

Cell Res 2017 Mar 28;27(3):416-439. Epub 2017 Feb 28.

State Key Laboratory of Medical Molecular Biology, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100005, China.

MicroRNA (miRNA) biogenesis is finely controlled by complex layers of post-transcriptional regulators, including RNA-binding proteins (RBPs). Here, we show that an RBP, QKI5, activates the processing of primary miR-124-1 (pri-124-1) during erythropoiesis. QKI5 recognizes a distal QKI response element and recruits Microprocessor through interaction with DGCR8. Furthermore, the recruited Microprocessor is brought to pri-124-1 stem loops by a spatial RNA-RNA interaction between two complementary sequences. Thus, mutations disrupting their base-pairing affect the strength of QKI5 activation. When erythropoiesis proceeds, the concomitant decrease of QKI5 releases Microprocessor from pri-124-1 and reduces mature miR-124 levels to facilitate erythrocyte maturation. Mechanistically, miR-124 targets TAL1 and c-MYB, two transcription factors involved in normal erythropoiesis. Importantly, this QKI5-mediated regulation also gives rise to a unique miRNA signature, which is required for erythroid differentiation. Taken together, these results demonstrate the pivotal role of QKI5 in primary miRNA processing during erythropoiesis and provide new insights into how a distal element on primary transcripts affects miRNA biogenesis.
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http://dx.doi.org/10.1038/cr.2017.26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5339841PMC
March 2017