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1.
Cell ; 181(2): 271-280.e8, 2020 04 16.
Article in English | MEDLINE | ID: mdl-32142651

ABSTRACT

The recent emergence of the novel, pathogenic SARS-coronavirus 2 (SARS-CoV-2) in China and its rapid national and international spread pose a global health emergency. Cell entry of coronaviruses depends on binding of the viral spike (S) proteins to cellular receptors and on S protein priming by host cell proteases. Unravelling which cellular factors are used by SARS-CoV-2 for entry might provide insights into viral transmission and reveal therapeutic targets. Here, we demonstrate that SARS-CoV-2 uses the SARS-CoV receptor ACE2 for entry and the serine protease TMPRSS2 for S protein priming. A TMPRSS2 inhibitor approved for clinical use blocked entry and might constitute a treatment option. Finally, we show that the sera from convalescent SARS patients cross-neutralized SARS-2-S-driven entry. Our results reveal important commonalities between SARS-CoV-2 and SARS-CoV infection and identify a potential target for antiviral intervention.


Subject(s)
Betacoronavirus/metabolism , Coronavirus Infections/drug therapy , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/drug therapy , Protease Inhibitors/pharmacology , Serine Endopeptidases/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Virus Internalization/drug effects , Ammonium Chloride/pharmacology , Angiotensin-Converting Enzyme 2 , Animals , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , Betacoronavirus/chemistry , Betacoronavirus/genetics , COVID-19 , Cell Line , Coronavirus/chemistry , Coronavirus/genetics , Coronavirus/physiology , Coronavirus Infections/immunology , Coronavirus Infections/therapy , Drug Development , Esters , Gabexate/analogs & derivatives , Gabexate/pharmacology , Guanidines , Humans , Immunization, Passive , Leucine/analogs & derivatives , Leucine/pharmacology , Pandemics , Peptidyl-Dipeptidase A/chemistry , Receptors, Virus/chemistry , Receptors, Virus/metabolism , Severe acute respiratory syndrome-related coronavirus/physiology , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Vesiculovirus/genetics , COVID-19 Serotherapy
2.
Nucleic Acids Res ; 52(D1): D1569-D1578, 2024 Jan 05.
Article in English | MEDLINE | ID: mdl-37897338

ABSTRACT

PlantPAN 4.0 (http://PlantPAN.itps.ncku.edu.tw/) is an integrative resource for constructing transcriptional regulatory networks for diverse plant species. In this release, the gene annotation and promoter sequences were expanded to cover 115 species. PlantPAN 4.0 can help users characterize the evolutionary differences and similarities among cis-regulatory elements; furthermore, this system can now help in identification of conserved non-coding sequences among homologous genes. The updated transcription factor binding site repository contains 3428 nonredundant matrices for 18305 transcription factors; this expansion helps in exploration of combinational and nucleotide variants of cis-regulatory elements in conserved non-coding sequences. Additionally, the genomic landscapes of regulatory factors were manually updated, and ChIP-seq data sets derived from a single-cell green alga (Chlamydomonas reinhardtii) were added. Furthermore, the statistical review and graphical analysis components were improved to offer intelligible information through ChIP-seq data analysis. These improvements included easy-to-read experimental condition clusters, searchable gene-centered interfaces for the identification of promoter regions' binding preferences by considering experimental condition clusters and peak visualization for all regulatory factors, and the 20 most significantly enriched gene ontology functions for regulatory factors. Thus, PlantPAN 4.0 can effectively reconstruct gene regulatory networks and help compare genomic cis-regulatory elements across plant species and experiments.


Subject(s)
Databases, Genetic , Gene Expression Regulation, Plant , Plants , Promoter Regions, Genetic , Gene Regulatory Networks , Plants/genetics , Protein Binding
3.
FASEB J ; 38(7): e23591, 2024 Apr 15.
Article in English | MEDLINE | ID: mdl-38572579

ABSTRACT

CircRNAs are abnormally expressed in various cancers and play an important role in the occurrence and development of cancers. However, their biological functions and the underlying molecular mechanisms in pancreatic cancer (PC) metastasis are incompletely understood. Differentially expressed circRNAs were identified by second-generation transcriptome sequencing in three pairs of PC tissues and adjacent tissues. The expression and prognostic significance of hsa_circ_0007919 were evaluated by qRT-PCR and Kaplan-Meier survival curves. Gain- and loss-of-function assays were conducted to detect the role of hsa_circ_0007919 in PC metastasis in vitro. A lung metastasis model and IHC experiments were conducted to confirm the effects of hsa_circ_0007919 on tumor metastasis in vivo. Mechanistically, RNA immunoprecipitation and chromatin immunoprecipitation assays were conducted to explore the interplay among hsa_circ_0007919, Sp1, and the THBS1 promoter. hsa_circ_0007919 was significantly upregulated in PC tissues and cells and was correlated with lymph node metastasis, TNM stage, and poor prognosis. Knockdown of hsa_circ_0007919 significantly suppressed the migration and invasion of PC cells in vitro and inhibited tumor metastasis in vivo. However, overexpression of hsa_circ_0007919 exerted the opposite effects. Mechanistically, hsa_circ_0007919 could recruit the transcription factor Sp1 to inhibit THBS1 transcription, thereby facilitating PC metastasis. hsa_circ_0007919 can promote the metastasis of PC by inhibiting THBS1 expression. hsa_circ_0007919 may be a potential therapeutic target in PC.


Subject(s)
MicroRNAs , Pancreatic Neoplasms , Humans , Cell Line, Tumor , Cell Proliferation/genetics , Gene Expression Regulation, Neoplastic , MicroRNAs/genetics , Neoplasm Invasiveness/genetics , Pancreatic Neoplasms/genetics , RNA, Circular/genetics , RNA, Circular/metabolism
4.
BMC Surg ; 24(1): 31, 2024 Jan 23.
Article in English | MEDLINE | ID: mdl-38263014

ABSTRACT

BACKGROUND: Due to the great heterogeneity of gastric cancer (GC), the prognosis of patients within a stage is very different. Therefore, it is necessary to identify the high risk factors for postoperative recurrence and metastasis and take appropriate therapeutic strategies to improve the prognosis of patients. In this study, we aimed to explore the prognostic significance of preoperative and postoperative serum carcinoembryonic antigen (CEA), carbohydrate antigen 19 - 9 (CA19-9) and carbohydrate antigen 72 - 4 (CA72-4) in patients with stage I, II and III GC who underwent radical gastrectomy. METHODS: A total of 580 patients who underwent curative surgical resection and had not received neoadjuvant chemotherapy were included in this study. The relationship between clinicopathological features and recurrence was analysed. Survival analysis was performed by Kaplan-Meier curve. Univariate and multivariate Cox regression analyses were performed to determine prognostic factors in GC patients. RESULTS: Among patients with stage III GC, the recurrence free survival (RFS) and overall survival (OS) of patients with CA19-9>35 U/mL were significantly lower than those with CA19-9 ≤ 35 U/mL; CA19-9 was always a significant independent marker. CEA and CA72-4 were sometime useful to predict RFS or OS alternatively in the pre- or postoperative period. The only other independent significant factors for prognosis in our study were lymph node metastases for RFS and postoperative adjuvant chemotherapy for OS. CONCLUSION: Preoperative and postoperative CA19-9 values are independent risk factors for predicting prognosis in stage III GC after curative gastrectomy.


Subject(s)
CA-19-9 Antigen , Stomach Neoplasms , Humans , Prognosis , Carcinoembryonic Antigen , Gastrectomy
5.
Mol Cancer ; 22(1): 195, 2023 12 04.
Article in English | MEDLINE | ID: mdl-38044421

ABSTRACT

BACKGROUND: Circular RNAs (circRNAs) play important roles in the occurrence and development of cancer and chemoresistance. DNA damage repair contributes to the proliferation of cancer cells and resistance to chemotherapy-induced apoptosis. However, the role of circRNAs in the regulation of DNA damage repair needs clarification. METHODS: RNA sequencing analysis was applied to identify the differentially expressed circRNAs. qRT-PCR was conducted to confirm the expression of hsa_circ_0007919, and CCK-8, FCM, single-cell gel electrophoresis and IF assays were used to analyze the proliferation, apoptosis and gemcitabine (GEM) resistance of pancreatic ductal adenocarcinoma (PDAC) cells. Xenograft model and IHC experiments were conducted to confirm the effects of hsa_circ_0007919 on tumor growth and DNA damage in vivo. RNA sequencing and GSEA were applied to confirm the downstream genes and pathways of hsa_circ_0007919. FISH and nuclear-cytoplasmic RNA fractionation experiments were conducted to identify the cellular localization of hsa_circ_0007919. ChIRP, RIP, Co-IP, ChIP, MS-PCR and luciferase reporter assays were conducted to confirm the interaction among hsa_circ_0007919, FOXA1, TET1 and the LIG1 promoter. RESULTS: We identified a highly expressed circRNA, hsa_circ_0007919, in GEM-resistant PDAC tissues and cells. High expression of hsa_circ_0007919 correlates with poor overall survival (OS) and disease-free survival (DFS) of PDAC patients. Hsa_circ_0007919 inhibits the DNA damage, accumulation of DNA breaks and apoptosis induced by GEM in a LIG1-dependent manner to maintain cell survival. Mechanistically, hsa_circ_0007919 recruits FOXA1 and TET1 to decrease the methylation of the LIG1 promoter and increase its transcription, further promoting base excision repair, mismatch repair and nucleotide excision repair. At last, we found that GEM enhanced the binding of QKI to the introns of hsa_circ_0007919 pre-mRNA and the splicing and circularization of this pre-mRNA to generate hsa_circ_0007919. CONCLUSIONS: Hsa_circ_0007919 promotes GEM resistance by enhancing DNA damage repair in a LIG1-dependent manner to maintain cell survival. Targeting hsa_circ_0007919 and DNA damage repair pathways could be a therapeutic strategy for PDAC.


Subject(s)
Carcinoma, Pancreatic Ductal , MicroRNAs , Pancreatic Neoplasms , Humans , Gemcitabine , RNA, Circular/genetics , RNA, Circular/metabolism , RNA Precursors , Carcinoma, Pancreatic Ductal/drug therapy , Carcinoma, Pancreatic Ductal/genetics , Carcinoma, Pancreatic Ductal/metabolism , Pancreatic Neoplasms/drug therapy , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/metabolism , DNA Damage , MicroRNAs/genetics , Cell Proliferation/genetics , Cell Line, Tumor , Mixed Function Oxygenases/genetics , Proto-Oncogene Proteins/genetics , Hepatocyte Nuclear Factor 3-alpha/genetics
6.
J Exp Bot ; 74(17): 4949-4958, 2023 09 13.
Article in English | MEDLINE | ID: mdl-37523674

ABSTRACT

Long noncoding RNAs (lncRNAs) are regulatory RNAs involved in numerous biological processes. Many plant lncRNAs have been identified, but their regulatory mechanisms remain largely unknown. A resource that enables the investigation of lncRNA activity under various conditions is required because the co-expression between lncRNAs and protein-coding genes may reveal the effects of lncRNAs. This study developed JustRNA, an expression profiling resource for plant lncRNAs. The platform currently contains 1 088 565 lncRNA annotations for 80 plant species. In addition, it includes 3692 RNA-seq samples derived from 825 conditions in six model plants. Functional network reconstruction provides insight into the regulatory roles of lncRNAs. Genomic association analysis and microRNA target prediction can be employed to depict potential interactions with nearby genes and microRNAs, respectively. Subsequent co-expression analysis can be employed to strengthen confidence in the interactions among genes. Chromatin immunoprecipitation sequencing data of transcription factors and histone modifications were integrated into the JustRNA platform to identify the transcriptional regulation of lncRNAs in several plant species. The JustRNA platform provides researchers with valuable insight into the regulatory mechanisms of plant lncRNAs. JustRNA is a free platform that can be accessed at http://JustRNA.itps.ncku.edu.tw.


Subject(s)
MicroRNAs , RNA, Long Noncoding , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , MicroRNAs/genetics , MicroRNAs/metabolism , Gene Expression Regulation , Transcription Factors/metabolism , Gene Expression Profiling , RNA, Plant/genetics
7.
Cell Mol Life Sci ; 80(1): 20, 2022 Dec 28.
Article in English | MEDLINE | ID: mdl-36576581

ABSTRACT

Numerous mechanisms involved in promoting cancer cell survival under nutrient starvation have been described. Long noncoding RNAs (lncRNAs) have emerged as critical players in colorectal cancer (CRC) progression, but the role of lncRNAs in the progression of CRC under nutrient starvation has not been well clarified. Here, we identified a lncRNA, LINC01615, that was significantly upregulated in response to serum starvation. LINC01615 can contribute to the adaptation of CRC cells to serum-deprived conditions and enhance cell survival under similar conditions. LINC01615 activated the pentose phosphate pathway (PPP) under serum starvation, manifested as decreased ROS production and enhanced nucleotide and lipid synthesis. Glucose-6-phosphate dehydrogenase (G6PD) is a key rate-limiting enzyme of the PPP, and LINC01615 promoted G6PD expression by competitively binding with hnRNPA1 and facilitating G6PD pre-mRNA splicing. Moreover, we also found that serum starvation led to METTL3 degradation by inducing autophagy, which further increased the stability and level of LINC01615 in a m6A-dependent manner. LINC01615 knockdown combined with oxaliplatin achieved remarkable antitumor effects in PDO and PDX models. Collectively, our results demonstrated a novel adaptive survival mechanism permitting tumor cells to survive under limiting nutrient supplies and provided a potential therapeutic target for CRC.


Subject(s)
Colorectal Neoplasms , RNA, Long Noncoding , Humans , Pentose Phosphate Pathway/genetics , Cell Survival/genetics , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , Oxaliplatin , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/genetics , Colorectal Neoplasms/metabolism , Cell Line, Tumor , Cell Proliferation , Gene Expression Regulation, Neoplastic , Methyltransferases/genetics
8.
New Phytol ; 234(4): 1315-1331, 2022 05.
Article in English | MEDLINE | ID: mdl-35244216

ABSTRACT

High temperatures cause huge yield losses in rice. Heat-shock factors (Hsfs) are key transcription factors which regulate the expression of heat stress-responsive genes, but natural variation in and functional characterization of Hsfs have seldom been reported. A significant heat response locus was detected via a genome-wide association study (GWAS) using green leaf area as an indicative trait. A miniature inverted-repeat transposable element (MITE) in the promoter of a candidate gene, HTG3 (heat-tolerance gene on chromosome 3), was found to be significantly associated with heat-induced expression of HTG3 and heat tolerance (HT). The MITE-absent variant has been selected in heat-prone rice-growing regions. HTG3a is an alternatively spliced isoform encoding a functional Hsf, and experiments using overexpression and knockout rice lines showed that HTG3a positively regulates HT at both vegetative and reproductive stages. The HTG3-regulated genes were enriched for heat shock proteins and jasmonic acid signaling. Two heat-responsive JASMONATE ZIM-DOMAIN (JAZ) genes were confirmed to be directly upregulated by HTG3a, and one of them, OsJAZ9, positively regulates HT. We conclude that HTG3 plays an important role in HT through the regulation of JAZs and other heat-responsive genes. The MITE-absent allele may be valuable for HT breeding in rice.


Subject(s)
Oryza , Thermotolerance , Cyclopentanes , DNA Transposable Elements , Gene Expression Regulation, Plant , Genome-Wide Association Study , Heat-Shock Response/genetics , Oryza/genetics , Oryza/metabolism , Oxylipins , Plant Breeding , Plant Proteins/genetics , Plant Proteins/metabolism , Protein Isoforms/metabolism , Thermotolerance/genetics
9.
Langenbecks Arch Surg ; 407(7): 2789-2799, 2022 Nov.
Article in English | MEDLINE | ID: mdl-35635585

ABSTRACT

BACKGROUND: Recently, the efficacy and outcomes of total laparoscopic pancreaticoduodenectomy (TLPD) have been well established; however, specific data regarding the clinical outcomes of total laparoscopic versus open pancreaticoduodenectomy (OPD) are still limited. The present study aims to directly compare the clinical and oncological outcomes following TLPD versus OPD at a single institution. METHODS: The clinical data of 127 consecutive patients who underwent TLPD (n = 69) and OPD (n = 58) and were admitted to our department between January 2017 and June 2019 were analysed retrospectively. The short-term and oncological outcomes in the two groups were compared. RESULTS: Compared to the OPD group, the TLPD group experienced a longer operative time [(399.1 ± 77.9) min vs. (247.9 ± 61.8) min] and significantly earlier oral intake [5.0 (IQR, 4.0-6.0) days vs. 8.0 (IQR, 6.0-8.0) days], earlier postoperative exhaust [3.0 (IQR, 3.0-4.0) days vs. 4.0 (IQR, 4.0-4.5) days], earlier out-of-bed activity [2.0 (IQR, 1.0-2.3) days vs. 3.0 (IQR, 2.0-3.0) days], earlier nasogastric tube removal [5.5 (IQR, 4.0-7.8) days vs. 8.0 (IQR, 6.0-11.0) days] and shorter postoperative length of hospital stay [14.0 (IQR, 11.0-21.0) days vs. 16.0 (IQR, 12.0-25.0) days] (P < 0.05). The estimated blood loss [(334.4 ± 157.8) mL vs. (344.6 ± 259.1) mL], presence of clinically relevant postoperative pancreatic fistula (grade B/C, 5.8% vs. 5.2%) and the overall complication rate (23.2% vs. 25.9%) did not significantly differ between the two groups (P > 0.05). Regarding the oncological outcomes, there were no significant differences in pathological types, tumour size, lymph nodes harvested, tumour stages or resection margins, or in overall survival (OS) (56.9% vs. 53.2%, P = 0.704) or progression-free survival (PFS) (48.3% vs. 46.8%, P = 0.881) with a median 26-month follow-up. CONCLUSION: TLPD is a safe and feasible procedure in select patients after a certain learning curve. Compared with OPD, TLPD has equivalent short-term and oncological outcomes and offers the advantages of faster postoperative recovery and shorter length of hospital stay.


Subject(s)
Laparoscopy , Pancreatic Neoplasms , Humans , Pancreaticoduodenectomy/methods , Retrospective Studies , Pancreatic Neoplasms/pathology , Pancreatectomy , Laparoscopy/methods , Length of Stay , Postoperative Complications/epidemiology , Postoperative Complications/surgery
10.
BMC Musculoskelet Disord ; 23(1): 996, 2022 Nov 18.
Article in English | MEDLINE | ID: mdl-36401234

ABSTRACT

BACKGROUND: Previous studies have reported that vitamin D supplement could improve fracture healing, but evidence regarding the role of vitamin D supplements in spinal fusion was limited. Thus, this study aimed to evaluate the effectiveness of oral vitamin D supplements on fusion outcomes in patients undergoing lumbar spinal fusion. METHODS: This randomized, double-blind, parallel-designed, active-control trial included the patients who planned for elective lumbar spinal fusion. Eligible patients were randomly assigned to receive either daily vitamin D3 (cholecalciferol) 800 IU and daily calcium citrate 600 mg (experimental group) or only daily calcium citrate 600 mg (control group). All supplements were given from postoperative day 1 and lasted for 3 months. Primary outcome was postoperative 1-year fusion rate, and secondary outcomes included time to fusion, Oswestry Disability Index (ODI), and visual analogue scale (VAS) for pain. RESULTS: Among the included 34 patients (21 in the experimental group and 13 in the control group), baseline 25-hydroxyvitamin D (25[OHVitD) level was 26.7 (10.4) ng/ml. Preoperative prevalence of vitamin D deficiency and insufficiency were 23.5% and 47.1%, respectively. Postoperative 1-year fusion rate was not significantly different between the two groups (95.2% vs. 84.6%, P = 0.544). The experimental group had significantly shorter time to fusion (Kaplan-Meier estimated: 169 days vs. 185 days [interquartile range: 88-182 days vs. 176-324 days], log-rank test: P = 0.028), lower postoperative 6-month ODI (P < 0.001), and lower postoperative 6-month VAS (P < 0.001) than the control group. Time to fusion was significantly and negatively correlated with preoperative, postoperative 3-month, and 6-month 25(OH)VitD levels (all P < 0.01). CONCLUSION: The patient with vitamin D supplements had shorter time to fusion, better spinal function and less pain after elective spinal fusion. Further research is warranted to identify the patients who can benefit the most from vitamin D supplements and the appropriate dose of vitamin D supplements. TRIAL REGISTRATION: ClinicalTrials.gov, NCT05023122. Registered 20 August 2021. Retrospectively registered, http://clinicaltrials.gov/ct2/show/NCT03793530 .


Subject(s)
Spinal Diseases , Spinal Fusion , Humans , Spinal Fusion/adverse effects , Calcium Citrate , Vitamins , Vitamin D , Cholecalciferol , Spinal Diseases/surgery , Pain
11.
Mol Cancer ; 20(1): 114, 2021 09 08.
Article in English | MEDLINE | ID: mdl-34496888

ABSTRACT

BACKGROUND: Circular RNAs (circRNAs) play important roles in cancer progression and metabolism regulation. Serine/glycine metabolism supports the growth of cancer cells by contributing to their anabolic demands and epigenome as well as by regulating their redox state. However, the role of circRNA in the regulation of serine/glycine metabolism has not been well elucidated. METHODS: Microarray analysis was used to screen differentially expressed novel circRNAs. qRT-PCR and FISH were utilized to analyzed the expression of circMYH9. CCK8, colony formation and FACS were used to analyze proliferation of colorectal cancer (CRC) cells. Xenograft experiments were used to analyze tumor growth in vivo. RNA-sequencing, immunoblot and LC-MS were used to identify the downstream metabolic pathway of circMYH9. ChIRP, Mass Spectrometry, RIP and RNA pulldown were utilized to test the interaction between circMYH9, hnRNPA2B1 and p53 pre-mRNA. ChIP-qPCR was used to analyze the binding sites of HIF-1α. Chemically-induced CRC mice were generated to evaluate the role of circMYH9 in tumorigenesis. RESULTS: We identified an intron-derived circRNA, circMYH9, which was significantly upregulated in CRC tissues. A higher circMYH9 level correlated with shorter relapse-free survival and overall survival of CRC patients. CircMYH9 promoted serine/glycine metabolism, the NAD + /NADH ratio, and glutathione recycling and inhibited reactive oxygen species (ROS) in a p53-dependent manner, impacting tumour growth. Mechanistically, circMYH9 destabilized the pre-mRNA of p53 by recruiting hnRNPA2B1 in the nucleus. hnRNPA2B1 bound to N6-methyladenosine sites on the 3' untranslated region of p53 pre-mRNA and maintained its stability. Moreover, a lack of amino acids led to an elevated level of ROS, resulting in increased HIF1α, which promoted circMYH9 expression by binding to the promoter region. Furthermore, in vivo AAV9-mediated transfection of circMYH9 could drive chemically-induced carcinogenesis by suppressing p53 in mice. CONCLUSIONS: The overexpression of circMYH9 promotes CRC proliferation though modulating serine/glycine metabolism and redox homeostasis in a p53-dependent manner, and targeting circMYH9 and its pathway may be an effective strategy for the treatment of CRC.


Subject(s)
Colorectal Neoplasms/genetics , Colorectal Neoplasms/metabolism , Myosin Heavy Chains/genetics , Oxidation-Reduction , RNA, Circular/genetics , Serine/metabolism , Tumor Suppressor Protein p53/genetics , 3' Untranslated Regions , Adult , Aged , Aged, 80 and over , Amino Acid Substitution , Animals , Biomarkers, Tumor , Cell Line, Tumor , Colorectal Neoplasms/mortality , Colorectal Neoplasms/pathology , Female , Gene Expression Regulation, Neoplastic , Homeostasis , Humans , Male , Mice , Middle Aged , Models, Biological , RNA Interference , Transcriptome , Tumor Suppressor Protein p53/metabolism
12.
RNA Biol ; 18(12): 2183-2193, 2021 12.
Article in English | MEDLINE | ID: mdl-34313542

ABSTRACT

Currently, more than one hundred types of RNA modifications have been found, and many of these modifications are reversible and dynamically regulated. RNA modifications can regulate RNA stability and translation and are thus involved in multiple biological activities. Recently, RNA modifications have been shown to have important roles in the regulation of cell death. Cell death is a critical process that maintains tissue homoeostasis and is regulated by multiple pathways in response to specific stimuli. In this review, we summarize the current understanding of the roles of RNA modifications in cell death mediation and discuss the prospects of such research.Abbreviations: m6A, N6-Methyladenosine; m6Am, N6,2'-O-Dimethyladenosine; m1A, N1-Methyladenosine; m5C, 5-Methylcytosine; hm5C, 5-Hydroxymethylcytosine; Ψ, pseudouridine; A-to-I, adenosine-to- inosine; hnRNPs, heterogeneous nuclear ribonucleoproteins; MOMP, mitochondrial outer membrane permeabilization; DD, death domain; DISC, death-inducing signalling complex; DED, death effector domain; FADD, FAS-associated protein with the death domain; TRADD, TNF receptor-associated protein with death domain; CMA, chaperone- mediated autophagy; PE, phosphatidylethanolamine; AD, alzheimer's disease; AML, acute myeloid leukaemia; miR, microRNA; 6-OHDA, 6-hydroxydopamine hydrochloride; R-2HG, R-2-hydroxyglutarate; IRES, internal ribosome entry site; BMSCs, bone-derived mesenchymal stem cells; NPCs, nucleus pulposus cells; HsCG, human chorionic gonadotropin; snoRNAs, small nucleolar RNAs; ER, endoplasmic reticulum; lncRNAs, long noncoding RNAs; TNM, tumour-node-metastasis.


Subject(s)
5-Methylcytosine/analogs & derivatives , 5-Methylcytosine/metabolism , Adenosine/analogs & derivatives , RNA, Messenger/chemistry , Adenosine/metabolism , Animals , Cell Death , Humans , RNA Processing, Post-Transcriptional , RNA Stability , Signal Transduction
13.
Plant Cell Physiol ; 61(6): 1204-1212, 2020 Jun 01.
Article in English | MEDLINE | ID: mdl-32181856

ABSTRACT

Small RNA (sRNA), such as microRNA (miRNA) and short interfering RNA, are well-known to control gene expression based on degradation of target mRNA in plants. A considerable amount of research has applied next-generation sequencing (NGS) to reveal the regulatory pathways of plant sRNAs. Consequently, numerous bioinformatics tools have been developed for the purpose of analyzing sRNA NGS data. However, most methods focus on the study of sRNA expression profiles or novel miRNAs predictions. The analysis of sRNA target genes is usually not integrated into their pipelines. As a result, there is still no means available for identifying the interaction mechanisms between host and virus or the synergistic effects between two viruses. For the present study, a comprehensive system, called the Small RNA Illustration System (sRIS), has been developed. This system contains two main components. The first is for sRNA overview analysis and can be used not only to identify miRNA but also to investigate virus-derived small interfering RNA. The second component is for sRNA target prediction, and it employs both bioinformatics calculations and degradome sequencing data to enhance the accuracy of target prediction. In addition, this system has been designed so that figures and tables for the outputs of each analysis can be easily retrieved and accessed, making it easier for users to quickly identify and quantify their results. sRIS is available at http://sris.itps.ncku.edu.tw/.


Subject(s)
Genome, Plant/genetics , High-Throughput Nucleotide Sequencing/methods , Plants/genetics , RNA, Plant/genetics , RNA, Small Untranslated/genetics , Genomic Library , MicroRNAs/genetics , MicroRNAs/physiology , RNA, Plant/physiology , RNA, Small Interfering/genetics , RNA, Small Interfering/physiology , RNA, Small Untranslated/physiology , Sequence Analysis, RNA/methods
14.
Plant Cell Physiol ; 61(10): 1818-1827, 2020 Oct 01.
Article in English | MEDLINE | ID: mdl-32898258

ABSTRACT

Co-expressed genes tend to have regulatory relationships and participate in similar biological processes. Construction of gene correlation networks from microarray or RNA-seq expression data has been widely applied to study transcriptional regulatory mechanisms and metabolic pathways under specific conditions. Furthermore, since transcription factors (TFs) are critical regulators of gene expression, it is worth investigating TFs on the promoters of co-expressed genes. Although co-expressed genes and their related metabolic pathways can be easily identified from previous resources, such as EXPath and EXPath Tool, this information is not simultaneously available to identify their regulatory TFs. EXPath 2.0 is an updated database for the investigation of regulatory mechanisms in various plant metabolic pathways with 1,881 microarray and 978 RNA-seq samples. There are six significant improvements in EXPath 2.0: (i) the number of species has been extended from three to six to include Arabidopsis, rice, maize, Medicago, soybean and tomato; (ii) gene expression at various developmental stages have been added; (iii) construction of correlation networks according to a group of genes is available; (iv) hierarchical figures of the enriched Gene Ontology (GO) terms are accessible; (v) promoter analysis of genes in a metabolic pathway or correlation network is provided; and (vi) user's gene expression data can be uploaded and analyzed. Thus, EXPath 2.0 is an updated platform for investigating gene expression profiles and metabolic pathways under specific conditions. It facilitates users to access the regulatory mechanisms of plant biological processes. The new version is available at http://EXPath.itps.ncku.edu.tw.


Subject(s)
Databases, Genetic , Gene Expression Regulation, Plant , Gene Expression , Arabidopsis/genetics , Arabidopsis/metabolism , Genes, Plant , High-Throughput Screening Assays , Solanum lycopersicum/genetics , Solanum lycopersicum/metabolism , Medicago/genetics , Medicago/metabolism , Oligonucleotide Array Sequence Analysis , Oryza/genetics , Oryza/metabolism , Glycine max/genetics , Glycine max/metabolism , Transcription Factors/genetics , Zea mays/genetics , Zea mays/metabolism
15.
BMC Cardiovasc Disord ; 20(1): 283, 2020 06 10.
Article in English | MEDLINE | ID: mdl-32522169

ABSTRACT

BACKGROUND: Evidence on association between body composition and outcomes of transcatheter aortic valve implantation (TAVI) is limited for Asian patients. This study investigated the prognostic role of body composition parameters in Taiwanese patients undergoing TAVI. MATERIALS AND METHODS: Data of consecutive patients undergoing TAVI for severe aortic stenosis between May 1, 2010 and August 31, 2019 were prospectively collected in this observational study. The association between body composition parameters (body mass index [BMI], body surface area [BSA], lean body mass [LBM], and LBM index) and cumulative mortality was analyzed using Cox proportional hazard regression model. RESULTS: A total of 221 patients (mean age 81.4 years), including 125 (56.6%) males, were included with median follow-up duration of 23.8 months. In males, multivariate analysis revealed that higher BMI (P = 0.035), BMI ≥ 20 kg/m2 (P = 0.026), and higher LBM index (P = 0.023) significantly predicted lower overall all-cause cumulative mortality. In females, none of the body composition parameters was significantly associated with all-cause cumulative mortality. Paradoxical association between BMI and estimated all-cause cumulative mortality was only significant among male patients. CONCLUSION: In Taiwanese TAVI patients, the prognostic effects of BMI and LBM index on cumulative mortality were only observed in males, not in females. Sex differences must be considered when stratifying risk among patients undergoing TAVI.


Subject(s)
Aortic Valve Stenosis/surgery , Body Composition , Health Status Disparities , Transcatheter Aortic Valve Replacement , Adiposity , Aged , Aged, 80 and over , Aortic Valve Stenosis/diagnostic imaging , Aortic Valve Stenosis/mortality , Aortic Valve Stenosis/physiopathology , Body Mass Index , Body Surface Area , Databases, Factual , Female , Humans , Male , Retrospective Studies , Risk Assessment , Risk Factors , Sex Factors , Taiwan , Transcatheter Aortic Valve Replacement/adverse effects , Transcatheter Aortic Valve Replacement/mortality , Treatment Outcome
16.
Eur Spine J ; 29(7): 1590-1596, 2020 07.
Article in English | MEDLINE | ID: mdl-32342281

ABSTRACT

PURPOSE: This study aimed to demonstrate that the augmented reality computer-assisted spine surgery (ARCASS) system is clinically feasible for percutaneous vertebroplasty (PVP). METHODS: This prospective case-control study included the patients undergoing PVP under the assistance of the ARCASS system between July 1, 2013, and October 31, 2014. The control group was the age- and gender-matched patients who underwent standard PVP and met the same eligible criteria as the case group. Primary outcome was the frequency of fluoroscopy. Secondary outcomes were the accuracy of bony entry point and operative time. RESULTS: Eighteen patients were included in this study: 9 patients with 11 levels of lesions in the ARCASS group and 9 patients with 10 levels of lesions in the control group. Compared with the control group, the ARCASS group had significantly less frequency of fluoroscopy (6 vs. 18, P < 0.001) and shorter operative time (78 vs. 205 s, P < 0.001) during the process of entry point identification and local anesthesia, which started from the registration of skin entry point at lesion site to the end of bony entry point identification. Regarding accuracy, the ARCASS group had significant greater proportion of 'good' entry point than the control group on lateral views (81.8% vs. 30.0%, P = 0.028) and anteroposterior views (72.7% vs. 20.0%, P = 0.020). CONCLUSION: This study revealed that the ARCASS system was clinically feasible for PVP. The guidance of ARCASS system provided more accurate bony entry point with reduced operative time and unnecessary radiation exposure.


Subject(s)
Augmented Reality , Surgery, Computer-Assisted , Vertebroplasty , Computers , Feasibility Studies , Fluoroscopy , Humans , Prospective Studies
17.
J Infect Dis ; 219(10): 1596-1604, 2019 04 19.
Article in English | MEDLINE | ID: mdl-30776304

ABSTRACT

We analyzed the virulence of pandemic H1N1 2009 influenza A viruses in vivo and in vitro. Selected viruses isolated in 2009, 2010, 2014, and 2015 were assessed using an aerosol-mediated high-dose infection model for pigs as well as air-liquid interface cultures of differentiated airway epithelial cells. Using a dyspnea score, rectal temperature, lung lesions, and viral load in the lung as parameters, the strains from 2014-2015 were significantly less virulent than the strains isolated in 2009-2010. In vitro, the viruses from 2009-2010 also differed from the 2014-2015 viruses by increased release of infectious virus, a more pronounced loss of ciliated cells, and a reduced thickness of the epithelial cell layer. Our in vivo and in vitro results reveal an evolution of A(H1N1)pdm09 viruses toward lower virulence. Our in vitro culture system can be used to predict the virulence of influenza viruses.


Subject(s)
Influenza A Virus, H1N1 Subtype/pathogenicity , Lung/virology , Orthomyxoviridae Infections/veterinary , Virulence , Animals , Cells, Cultured , Epithelial Cells/virology , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/physiology , Orthomyxoviridae Infections/virology , Sus scrofa , Viral Load/veterinary
18.
Infect Immun ; 87(8)2019 08.
Article in English | MEDLINE | ID: mdl-31138613

ABSTRACT

Streptococcus suis is an important zoonotic pathogen which can infect humans and pigs worldwide, posing a potential risk to global public health. Suilysin, a pore-forming cholesterol-dependent cytolysin, is considered to play an important role in the pathogenesis of S. suis infections. It is known that infection with influenza A viruses may favor susceptibility to secondary bacterial infection, resulting in more severe disease and increased mortality. However, the molecular mechanisms underlying these coinfections are incompletely understood. Applying highly differentiated primary porcine respiratory epithelial cells grown under air-liquid interface (ALI) conditions, we analyzed the contribution of swine influenza viruses (SIV) to the virulence of S. suis, with a special focus on its cytolytic toxin, suilysin. We found that during secondary bacterial infection, suilysin of S. suis contributed to the damage of well-differentiated respiratory epithelial cells in the early stage of infection, whereas the cytotoxic effects induced by SIV became prominent at later stages of infection. Prior infection by SIV enhanced the adherence to and colonization of porcine airway epithelial cells by a wild-type (wt) S. suis strain and a suilysin-negative S. suis mutant in a sialic acid-dependent manner. A striking difference was observed with respect to bacterial invasion. After bacterial monoinfection, only the wt S. suis strain showed an invasive phenotype, whereas the mutant remained adherent. When the epithelial cells were preinfected with SIV, the suilysin-negative mutant also showed an invasion capacity. Therefore, we propose that coinfection with SIV may compensate for the lack of suilysin in the adherence and invasion process of suilysin-negative S. suis.


Subject(s)
Bacterial Adhesion/physiology , Coinfection/microbiology , Hemolysin Proteins/physiology , Lung/microbiology , Orthomyxoviridae Infections/microbiology , Streptococcus suis/pathogenicity , Animals , Cells, Cultured , Dogs , Epithelial Cells/microbiology , Swine
20.
Emerg Infect Dis ; 25(12): 2295-2298, 2019 12.
Article in English | MEDLINE | ID: mdl-31742519

ABSTRACT

We detected a highly pathogenic avian influenza A(H5N8) virus in lung samples of 2 gray seals (Halichoerus grypus) stranded on the Baltic coast of Poland in 2016 and 2017. This virus, clade 2.3.4.4 B, was closely related to avian H5N8 viruses circulating in Europe at the time.


Subject(s)
Influenza A Virus, H5N8 Subtype , Orthomyxoviridae Infections/epidemiology , Orthomyxoviridae Infections/virology , Seals, Earless/virology , Animals , Baltic States , Hemagglutinin Glycoproteins, Influenza Virus , Influenza A Virus, H5N8 Subtype/classification , Influenza A Virus, H5N8 Subtype/genetics , Influenza A Virus, H5N8 Subtype/isolation & purification , Male , Oceans and Seas , Phylogeny , Poland
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