DOCSLIB.ORG

Prognosis-Related Autophagy Genes in Female Lung Adenocarcinoma

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Prognosis-Related Autophagy Genes in Female Lung Adenocarcinoma Prognosis-Related Autophagy Genes in Female Lung Adenocarcinoma Zhongxiang Liu rst people's hospital of yancheng Haicheng Tang Shanghai Public Health Clinical Center Yongqian Jiang rst people's hospital of yancheng Xiaopeng Zhan Shanghai East Hospital Sheng Kang Shanghai East Hospital Koudong Zhang ( [email protected] ) First People's Hospital of Yancheng Li Lin Shanghai East Hospital Research Keywords: Autophagy genes, Prognosis, Female lung adenocarcinoma, Risk score Posted Date: August 10th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-53994/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/15 Abstract Background: To screen the prognosis-related autophagy genes of female lung adenocarcinoma by the transcriptome data and clinical data from TCGA database. Methods: In this study, Screen meaningful female lung adenocarcinoma differential genes in TCGA, use univariate COX proportional regression model to select genes related to prognosis, and establish the best risk model. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied for carrying out bioinformatics analysis of gene function. Results: The gene expression and clinical data of 260 female lung adenocarcinoma patient samples were downloaded from TCGA. 12 down-regulated genes: NRG3, DLC1, NLRC4, DAPK2, HSPB8, PPP1R15A, FOS, NRG1, PRKCQ, GRID1, MAP1LC3C, GABARAPL1. Up-regulated 15 genes: PARP1, BNIP3, P4HB, ATIC, IKBKE, ITGB4, VMP1, PTK6, EIF4EBP1, GAPDH, ATG9B, ERO1A, TMEM74, CDKN2A, BIRC5. GO and KEGG analysis showed that these genes were signicantly associated with autophagy and mitochondria (animals). Multi-factor COX analysis of autophagy-related genes showed that ITGA6, ERO1A, FKBP1A, BAK1, CCR2, FADD, EDEM1, ATG10, ATG4A, DLC1, VAMP7, ST13 were identied as independent prognostic indicators. According to the multivariate COX proportional hazard regression model, there was a signicant difference in the survival rate observed between the high-risk group (n=124) and the low-risk group (n=126) during the 10-year follow-up (p<0.05). Univariate COX analysis showed that tumor stage, T, M and N stages, and risk score were all related to the survival rate of female lung adenocarcinoma patients. Multivariate COX analysis found that autophagy-related risk scores were independent predictors, with an AUC value of 0.842. At last, there are autophagy genes differentially expressed among various clinicopathological parameters: ATG4A, BAK1, CCR2, DLC1, ERO1A, FKBP1A, ITGA6. Conclusion: The risk score can be used as an independent prognostic indicator for female patients with lung adenocarcinoma. The autophagy genes ITGA6, ERO1A, FKBP1A, BAK1, CCR2, FADD, EDEM1, ATG10, ATG4A, DLC1, VAMP7, ST13 were identied as prognostic genes in female lung adenocarcinoma, which may be the targets of treatment in the future. Background Lung cancer is the most common malignancies with high morbidity worldwide, which represents the second leading cause of cancer-related deaths[1]. Data from the National Cancer Registry[2] show a signicant increase in lung cancer incidence in women and a gradual decrease in men, while men have an overall survival advantage in the patients with non-small cell lung cancer (NSCLC)[3]. Although current treatment approaches, including maximum safe resection, chemotherapy, radiotherapy and targeted therapy, have been adopted[4], the survival time has not improved signicantly, and the ve-year survival rate is 4% − 17%[5]. Despite the progress of experimental technologies and therapeutic regimens in the eld, lung cancer remains incurable. It is thus necessary to explore the novel therapeutic targets or treatment methods. Page 2/15 Autophagy is a genetically conserved cellular process and widely exists in eukaryotic cells, which is one of the necessary ways of organelle renewal and metabolism dynamic balance[6], especially for maintaining homeostasis in vivo and tumor growth of lung cancer, thus it prevents the p53 activation, growth arrest, apoptosis, senescence and immune response activation. Autophagy in NSCLC can maintain mitochondrial mass and regulate its abundance, while the genetic deciency of essential autophagy genes in tumors will reduce tumor growth[7]. Even DNA methylation of autophagy genes plays an important role in cancer development, and the epigenetic-mediated aberrant gene silencing has been considered to be closely related to the pathogenesis of cancers, including lung cancer[8].Generally, autophagy is thought to prevent carcinogenesis by eliminating oncogenic protein substrates, misfolded proteins, and damaged organelles[9]. Therefore, more and more studies have shown that autophagy has an important role in NSCLC[10]. Methods Gene expression data, clinical characteristics and survival information of 260 samples from female patients with lung adenocarcinoma were downloaded from TCGA database on June 02, 2020. A total of 221 autophagy-related genes were extracted from Human Autophagy Database (HADb http:/ /www.autop hagy.lu/index.html). Statistical analysis A series of gene function enrichment analysis was performed After screening the differentially expressed autophagy-related genes, to determine the main biological properties. Univariate Cox proportional hazard regression analysis was used to assess the association between overall survival (OS) and the selected autophagy genes. Next, multivariate Cox proportional hazard regression analysis was performed on the identied autophagy genes. Independent prognostic factors were determined by multivariate Cox proportional hazards regression analysis, and regression coecient and risk ratio (HR) were calculated by Cox regression model for establishing an autophagy related model, which can be used as the prognosis model of female lung adenocarcinoma. The risk score of patients was divided into high-risk group and low-risk group according to the median score. Survival curve, risk curve, ROC curve of risk score and other clinical characteristics, and beeswarm of correlation between autophagy gene, the risk score and clinical characteristics were drawn. All the statistical analyses including the different expression of autophagy-related genes in univariate and multivariate Cox regression models, ROC curve and K-M survival were performed using R version 3.6.6 (The R Foundation for Statistical Computing). GO plot software package was used to Gene Ontology (GO) enrichment analysis, and the same tool is also used for the enrichment analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. P < 0.05 was used as the signicant threshold. Results Page 3/15 Identication analysis of ATGs The expression values of 221 ATGs were integrated from the female patients with lung adenocarcinoma, and 12 downregulated genes and 15 upregulated genes were identied. Boxplots (Figure 1a), Heat maps (Figure 1b), and volcano maps (Figure 1c) were used to reveal the expression patterns of these differentially expressed genes in tumor and non-tumor tissues. Functional enrichment analysis A total of 27 differentially expressed genes were performed functional analysis to provide biological function for these genes. In order to inquire the potential signal pathways related 27 ATGs in female lung adenocarcinoma, we analyzed them with GO and KEGG. GO analysis Figure 2a-cshowed that these ATGs were enriched in some basic biological processes (BP), including the process of autophagy and apoptotic signaling pathways. The cellular components affected those of autophagy and mitochondria. Based on molecular functions, the genes were most enriched in cellular response to oxidative stress, protein phosphatase binding, and phosphatase binding. KEGG analysis Figure 3a,bshowed that the 27 ATGs were signicantly associated with autophagy and mitochondria (animals), and the most scores of enriched pathways were greater than zero, indicating that these pathways were more likely to be enhanced. Construction of prognostic markers in female LUAD 28 ATGs were analyzed by univariate Cox regression. 8 genes were identied as protective factors (HR<1), while another 20 genes were identied as risk factors (HR>1). The 28 genes were further analyzed by multivariate Cox regression analysis, and nally 12 genes ( ITGA6ERO1AFKBP1ABAK1CCR2FADD EDEM1ATG10ATG4ADLC1VAMP7ST13) were identied as independent prognostic indicators, which might be helpful in predicting prognosis. The 12 genes were further analyzed by multivariate Cox regression analysis, the expression coecients of each independent risk gene were obtained and shown in table 1, and nally the model for predicting prognosis based was developed using the following formulas: prognostic index (PI) = (-0.162*ITGA6 expression level) + (0.466*ERO1A expression level) + (0.872*FKBP1A expression level) + (0.373*BAK1 expression level) + (-0.392*CCR2 expression level) + (0.416*The expression level of FADD) + (-0.625*EDEM1) + (0.778*ATG1 0 expression level) + (-0.899*ATG4A expression level) + (0.399*DLC1 expression level) + (0.367*VAMP7 expression level) + (0.572*ST13 expression level). The risk score of each patient was calculated on the basis of the relevant mRNA expression level and risk coecient of each ATG. The risk score is used to predict the prognosis of female LUAD, and the median risk score is the critical value to divide patients into high-risk and low-risk groups (Figure 5b). Heatmap was drawn to show gene expression proles in high-risk and low-risk female LUAD groups (Figure 5c). The genes with HR>1 were
Load more

Recommended publications
  • Novel Insights Into Autophagy from Multicellular Model Systems
    Feature Review Eaten alive: novel insights into autophagy from multicellular model systems 1 2 Hong Zhang and Eric H. Baehrecke 1 Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China 2 Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA Autophagy delivers cytoplasmic material to lysosomes are essential for autophagosome formation [7,8]. Remark- for degradation. First identified in yeast, the core genes ably, the core autophagy machinery that is encoded by that control this process are conserved in higher organ- these genes is conserved between yeast and humans isms. Studies of mammalian cell cultures have expanded [6]. Many studies of immortalized mammalian cell lines our understanding of the core autophagy pathway, but indicate that, as in yeast, nutrient-limiting conditions cannot reveal the unique animal-specific mechanisms induce autophagy that is dependent on ATG genes. How- for the regulation and function of autophagy. Multicel- ever, several aspects of the autophagy pathway in higher lular organisms have different types of cells that possess eukaryotes are distinct from that in yeast. In yeast, all distinct composition, morphology, and organization of autophagosomes arise from the single perivacuolar preau- intracellular organelles. In addition, the autophagic ma- tophagosomal structure (PAS). In higher eukaryotes, there chinery integrates signals from other cells and environ- is no evidence for a PAS and isolation membranes can be mental conditions to maintain cell, tissue and organism generated simultaneously at multiple sites, implicating homeostasis. Here, we highlight how studies of autop- more complex sources for autophagosomal membranes. hagy in flies and worms have identified novel core Indeed, the endoplasmic reticulum (ER), mitochondria, autophagy genes and mechanisms, and provided insight plasma membrane, and recycling endosomes have been into the context-specific regulation and function of shown to contribute to autophagosomal membranes autophagy.
    [Show full text]
  • Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (3Rd Edition)
    AUTOPHAGY 2016, VOL. 12, NO. 1, 1–222 http://dx.doi.org/10.1080/15548627.2015.1100356 EDITORIAL Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) Daniel J Klionsky1745,1749*, Kotb Abdelmohsen840, Akihisa Abe1237, Md Joynal Abedin1762, Hagai Abeliovich425, Abraham Acevedo Arozena789, Hiroaki Adachi1800, Christopher M Adams1669, Peter D Adams57, Khosrow Adeli1981, Peter J Adhihetty1625, Sharon G Adler700, Galila Agam67, Rajesh Agarwal1587, Manish K Aghi1537, Maria Agnello1826, Patrizia Agostinis664, Patricia V Aguilar1960, Julio Aguirre-Ghiso784,786, Edoardo M Airoldi89,422, Slimane Ait-Si-Ali1376, Takahiko Akematsu2010, Emmanuel T Akporiaye1097, Mohamed Al-Rubeai1394, Guillermo M Albaiceta1294, Chris Albanese363, Diego Albani561, Matthew L Albert517, Jesus Aldudo128, Hana Algul€ 1164, Mehrdad Alirezaei1198, Iraide Alloza642,888, Alexandru Almasan206, Maylin Almonte-Beceril524, Emad S Alnemri1212, Covadonga Alonso544, Nihal Altan-Bonnet848, Dario C Altieri1205, Silvia Alvarez1497, Lydia Alvarez-Erviti1395, Sandro Alves107, Giuseppina Amadoro860, Atsuo Amano930, Consuelo Amantini1554, Santiago Ambrosio1458, Ivano Amelio756, Amal O Amer918, Mohamed Amessou2089, Angelika Amon726, Zhenyi An1538, Frank A Anania291, Stig U Andersen6, Usha P Andley2079, Catherine K Andreadi1690, Nathalie Andrieu-Abadie502, Alberto Anel2027, David K Ann58, Shailendra Anoopkumar-Dukie388, Manuela Antonioli832,858, Hiroshi Aoki1791, Nadezda Apostolova2007, Saveria Aquila1500, Katia Aquilano1876, Koichi Araki292, Eli Arama2098,
    [Show full text]
  • Ryanodine Binding to Ryr1. Final Report Edward M
    Evaluation of GSK2487213A on [3H]Ryanodine Binding to RyR1. Final Report Edward M. Balog, PhD School of Applied Physiology Georgia Institute of Technology December 17, 2010 1 Summary The effects of GSK2487213A (213A) on RyR1 function was assessed via skeletal muscle heavy sarcoplasmic reticulum (HSR) [3H]ryanodine binding. 213A did not affect HSR ryanodine binding when Ca2+ was the sole RyR1 regulator. Stripping HSR of FKBP12.0, via treatment with FK506, increased Ca2+-activated ryanodine binding. Exogenous FKBP12.0 alone or in combination with 213A and or reducing agents failed to reverse the effects prior exposure to FK506. Including FK506 in the HSR [3H]ryanodine binding buffer dose-dependently increased ryanodine binding. 213A did not alter the FK506 dose response. Treating HSR with the nitric oxide donor, NOR-3, did not substantially reduce the FKBP12.0 content of the HSR. Prior exposure to NOR-3 enhanced Ca2+ stimulated HSR ryanodine binding. 213A reversed the NOR-3 activation of RyR1. These results suggest that 213A reverses nitrosylation-induced activation of RyR1 and the inhibition does not occur via stabilizing the interaction between RyR1 and FKBP12.0. Introduction Ryanodine receptors (RyR) are endo/sarcoplamic reticulum (SR) resident Ca2+ selective channels that form the efflux pathway for the release of Ca2+ from the SR to initiate muscle contraction. Isoform 1 (RyR1) is the predominate form in skeletal muscle, RyR2 is the predominate form in the heart while RyR3 has a widespread distribution. The channels are regulated by numerous endogenous effectors including ions primarily Ca2+ and Mg2+, metabolites such as the adenine nucleotides and accessory proteins including calmodulin and the FK506-binding proteins (FKBP).
    [Show full text]
  • TMEM95 Is a Sperm Membrane Protein Essential for Mammalian
    RESEARCH ARTICLE TMEM95 is a sperm membrane protein essential for mammalian fertilization Ismael Lamas-Toranzo1†, Julieta G Hamze2†, Enrica Bianchi3, Beatriz Ferna´ ndez-Fuertes4,5, Serafı´nPe´ rez-Cerezales1, Ricardo Laguna-Barraza1, Rau´l Ferna´ ndez-Gonza´ lez1, Pat Lonergan4, Alfonso Gutie´ rrez-Ada´ n1, Gavin J Wright3, Marı´aJime´ nez-Movilla2*, Pablo Bermejo-A´ lvarez1* 1Animal Reproduction Department, INIA, Madrid, Spain; 2Department of Cell Biology and Histology, Medical School, University of Murcia, IMIB-Arrixaca, Murcia, Spain; 3Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge, United Kingdom; 4School of Agriculture and Food Science, University College Dublin, Dublin, Ireland; 5Department of Biology, Faculty of Sciences, Institute of Food and Agricultural Technology, University of Girona, Girona, Spain Abstract The fusion of gamete membranes during fertilization is an essential process for sexual reproduction. Despite its importance, only three proteins are known to be indispensable for sperm- egg membrane fusion: the sperm proteins IZUMO1 and SPACA6, and the egg protein JUNO. Here we demonstrate that another sperm protein, TMEM95, is necessary for sperm-egg interaction. TMEM95 ablation in mice caused complete male-specific infertility. Sperm lacking this protein were morphologically normal exhibited normal motility, and could penetrate the zona pellucida and bind to the oolemma. However, once bound to the oolemma, TMEM95-deficient sperm were unable to fuse with the egg membrane or penetrate into the ooplasm, and fertilization could only be achieved by mechanical injection of one sperm into the ooplasm, thereby bypassing membrane *For correspondence: fusion. These data demonstrate that TMEM95 is essential for mammalian fertilization. [email protected] (Mı´Je´-M); [email protected] (PB-A´ ) †These authors contributed equally to this work Introduction In sexually reproducing species, life begins with the fusion of two gametes during fertilization.
    [Show full text]
  • Proteomic Analysis of Exosome-Like Vesicles Derived from Breast Cancer Cells
    ANTICANCER RESEARCH 32: 847-860 (2012) Proteomic Analysis of Exosome-like Vesicles Derived from Breast Cancer Cells GEMMA PALAZZOLO1, NADIA NINFA ALBANESE2,3, GIANLUCA DI CARA3, DANIEL GYGAX4, MARIA LETIZIA VITTORELLI3 and IDA PUCCI-MINAFRA3 1Institute for Biomedical Engineering, Laboratory of Biosensors and Bioelectronics, ETH Zurich, Switzerland; 2Department of Physics, University of Palermo, Palermo, Italy; 3Centro di Oncobiologia Sperimentale (C.OB.S.), Oncology Department La Maddalena, Palermo, Italy; 4Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland FHNW, Muttenz, Switzerland Abstract. Background/Aim: The phenomenon of membrane that vesicle production allows neoplastic cells to exert different vesicle-release by neoplastic cells is a growing field of interest effects, according to the possible acceptor targets. For instance, in cancer research, due to their potential role in carrying a vesicles could potentiate the malignant properties of adjacent large array of tumor antigens when secreted into the neoplastic cells or activate non-tumoral cells. Moreover, vesicles extracellular medium. In particular, experimental evidence show could convey signals to immune cells and surrounding stroma that at least some of the tumor markers detected in the blood cells. The present study may significantly contribute to the circulation of mammary carcinoma patients are carried by knowledge of the vesiculation phenomenon, which is a critical membrane-bound vesicles. Thus, biomarker research in breast device for trans cellular communication in cancer. cancer can gain great benefits from vesicle characterization. Materials and Methods: Conditioned medium was collected The phenomenon of membrane release in the extracellular from serum starved MDA-MB-231 sub-confluent cell cultures medium has long been known and was firstly described by and exosome-like vesicles (ELVs) were isolated by Paul H.
    [Show full text]
  • Datasheet: VPA00601 Product Details
    Datasheet: VPA00601 Description: RABBIT ANTI FKBP1A Specificity: FKBP1A Format: Purified Product Type: PrecisionAb™ Polyclonal Isotype: Polyclonal IgG Quantity: 100 µl Product Details Applications This product has been reported to work in the following applications. This information is derived from testing within our laboratories, peer-reviewed publications or personal communications from the originators. Please refer to references indicated for further information. For general protocol recommendations, please visit www.bio-rad-antibodies.com/protocols. Yes No Not Determined Suggested Dilution Western Blotting 1/1000 PrecisionAb antibodies have been extensively validated for the western blot application. The antibody has been validated at the suggested dilution. Where this product has not been tested for use in a particular technique this does not necessarily exclude its use in such procedures. Further optimization may be required dependant on sample type. Target Species Human Product Form Purified IgG - liquid Preparation Rabbit polyclonal antibody purified by affinity chromatography Buffer Solution Phosphate buffered saline Preservative 0.09% Sodium Azide (NaN3) Stabilisers 2% Sucrose Immunogen Synthetic peptide directed towards the middle region of human FKBP1A External Database Links UniProt: P62942 Related reagents Entrez Gene: 2280 FKBP1A Related reagents Synonyms FKBP1, FKBP12 Specificity Rabbit anti Human FKBP1A antibody recognizes the peptidyl-prolyl cis-trans isomerase FKBP1A, also known as 12 kDa FK506-binding protein, 12 kDa FKBP, FKBP12-Exip3, PPIase FKBP1A, calstabin 1, immunophilin FKBP12, protein kinase C inhibitor 2 or rotamase. Page 1 of 2 The protein encoded by the FKBP1A gene is a member of the immunophilin protein family, which play a role in immunoregulation and basic cellular processes involving protein folding and trafficking.
    [Show full text]
  • Mouse Atg10 Conditional Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Atg10 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Atg10 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Atg10 gene (NCBI Reference Sequence: NM_025770 ; Ensembl: ENSMUSG00000021619 ) is located on Mouse chromosome 13. 8 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 7 (Transcript: ENSMUST00000022119). Exon 2 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Atg10 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-326J5 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from about 100% of the coding region. The knockout of Exon 2 will result in frameshift of the gene. The size of intron 1 for 5'-loxP site insertion: 15505 bp, and the size of intron 2 for 3'-loxP site insertion: 54005 bp. The size of effective cKO region: ~605 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 2 8 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Atg10 Homology arm cKO region loxP site Page 2 of 7 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • FKBP1A Sirna Set I FKBP1A Sirna Set I
    Catalog # Aliquot Size F37-911-05 3 x 5 nmol F37-911-20 3 x 20 nmol F37-911-50 3 x 50 nmol FKBP1A siRNA Set I siRNA duplexes targeted against three exon regions Catalog # F37-911 Lot # Z2037-46 Specificity Formulation FKBP1A siRNAs are designed to specifically knock-down The siRNAs are supplied as a lyophilized powder and human FKBP1A expression. shipped at room temperature. Product Description Reconstitution Protocol FKBP1A siRNA is a pool of three individual synthetic siRNA Briefly centrifuge the tubes (maximum RCF 4,000g) to duplexes designed to knock-down human FKBP1A mRNA collect lyophilized siRNA at the bottom of the tube. expression. Each siRNA is 19-25 bases in length. The gene Resuspend the siRNA in 50 µl of DEPC-treated water accession number is NM_000801. (supplied by researcher), which results in a 1x stock solution (10 µM). Gently pipet the solution 3-5 times to mix Gene Aliases and avoid the introduction of bubbles. Optional: aliquot FKBP12, FKBP1, PKC12, PKCI2, PPIASE, FKBP-12, FKBP12C 1x stock solutions for storage. Storage and Stability Related Products The lyophilized powder is stable for at least 4 weeks at room temperature. It is recommended that the Product Name Catalog Number lyophilized and resuspended siRNAs are stored at or FKBP1A Protein F37-30G below -20oC. After resuspension, siRNA stock solutions ≥2 µM can undergo up to 50 freeze-thaw cycles without significant degradation. For long-term storage, it is recommended that the siRNA is stored at -70oC. For most favorable performance, avoid repeated handling and multiple freeze/thaw cycles.
    [Show full text]
  • Identification of a Novel Autophagy-Related Gene Signature
    Identication of a novel autophagy-related gene signature for predicting metastasis and survival in patients with osteosarcoma Guangzhi Zhang Lanzhou University Second Hospital https://orcid.org/0000-0003-3193-0297 Yajun Deng Lanzhou University Second Hospital Zuolong Wu Lanzhou University Second Hospital Enhui Ren Lanzhou University Second Hospital Wenhua Yuan Lanzhou University Second Hospital Qiqi Xie ( [email protected] ) Lanzhou University Second Hospital https://orcid.org/0000-0003-4099-5287 Primary research Keywords: osteosarcoma, autophagy-related genes, signature, survival, metastasis Posted Date: March 26th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-19384/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/20 Abstract Background: Osteosarcoma (OS) is a bone malignant tumor that occurs in children and adolescents. Due to a lack of reliable prognostic biomarkers, the prognosis of OS patients is often uncertain. This study aimed to construct an autophagy-related gene signature to predict the prognosis of OS patients. Methods: The gene expression prole data of OS and normal muscle tissue samples were downloaded separately from the Therapeutically Applied Research To Generate Effective Treatments (TARGET) and Genotype-Tissue Expression (GTEx) databases . The differentially expressed autophagy-related genes (DEARGs) in OS and normal muscle tissue samples were screened using R software, before being subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. A protein-protein interaction (PPI) network was constructed and hub autophagy-related genes were screened. Finally, the screened autophagy-related genes were subjected to univariate Cox regression, Lasso Cox regression, survival analysis, and clinical correlation analysis.
    [Show full text]
  • The Functional and Pathologic Relevance of Autophagy Proteases
    The functional and pathologic relevance of autophagy proteases Álvaro F. Fernández, Carlos López-Otín J Clin Invest. 2015;125(1):33-41. https://doi.org/10.1172/JCI73940. Review Autophagy is a well-conserved catabolic process essential for cellular homeostasis. First described in yeast as an adaptive response to starvation, this pathway is also present in higher eukaryotes, where it is triggered by stress signals such as damaged organelles or pathogen infection. Autophagy is characterized at the cellular level by the engulfment of portions of the cytoplasm in double-membrane structures called autophagosomes. Autophagosomes fuse with lysosomes, resulting in degradation of the inner autophagosomal membrane and luminal content. This process is coordinated by complex molecular systems, including the ATG8 ubiquitin–like conjugation system and the ATG4 cysteine proteases, which are implicated in the formation, elongation, and fusion of these autophagic vesicles. In this Review, we focus on the diverse functional roles of the autophagins, a protease family formed by the four mammalian orthologs of yeast Atg4. We also address the dysfunctional expression of these proteases in several pathologic conditions such as cancer and inflammation and discuss potential therapies based on their modulation. Find the latest version: https://jci.me/73940/pdf The Journal of Clinical Investigation REVIEW SERIES: AUTOPHAGY Series Editor: Guido Kroemer The functional and pathologic relevance of autophagy proteases Álvaro F. Fernández and Carlos López-Otín Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain. Autophagy is a well-conserved catabolic process essential for cellular homeostasis. First described in yeast as an adaptive response to starvation, this pathway is also present in higher eukaryotes, where it is triggered by stress signals such as damaged organelles or pathogen infection.
    [Show full text]
  • Potential Sperm Contributions to the Murine Zygote Predicted by in Silico Analysis
    REPRODUCTIONRESEARCH Potential sperm contributions to the murine zygote predicted by in silico analysis Panagiotis Ntostis1,2, Deborah Carter3, David Iles1, John Huntriss1, Maria Tzetis2 and David Miller1 1Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, West Yorkshire, UK, 2Department of Medical Genetics, St. Sophia’s Children Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Attiki, Greece and 3Leeds Institute of Molecular Medicine, University of Leeds, Leeds, West Yorkshire, UK Correspondence should be addressed to D Miller; Email: [email protected] Abstract Paternal contributions to the zygote are thought to extend beyond delivery of the genome and paternal RNAs have been linked to epigenetic transgenerational inheritance in different species. In addition, sperm–egg fusion activates several downstream processes that contribute to zygote formation, including PLC zeta-mediated egg activation and maternal RNA clearance. Since a third of the preimplantation developmental period in the mouse occurs prior to the first cleavage stage, there is ample time for paternal RNAs or their encoded proteins potentially to interact and participate in early zygotic activities. To investigate this possibility, a bespoke next-generation RNA sequencing pipeline was employed for the first time to characterise and compare transcripts obtained from isolated murine sperm, MII eggs and pre-cleavage stage zygotes. Gene network analysis was then employed to identify potential interactions between paternally and maternally derived factors during the murine egg-to-zygote transition involving RNA clearance, protein clearance and post-transcriptional regulation of gene expression. Our in silico approach looked for factors in sperm, eggs and zygotes that could potentially interact co-operatively and synergisticallyp during zygote formation.
    [Show full text]
  • Molecular Mechanism and Regulation of Autophagy in Saccharomyces Cerevisiae
    Molecular Mechanism and Regulation of Autophagy in Saccharomyces cerevisiae by Zhiyuan Yao A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Molecular, Cellular and Developmental Biology) in the University of Michigan 2018 Doctoral Committee: Professor Daniel J. Klionsky, Chair Professor Laura Olsen Professor Lois S. Weisman Professor Haoxing Xu Zhiyuan Yao [email protected] ORCID iD: 0000-0002-5759-9822 © Zhiyuan Yao 2018 Dedication This thesis is dedicated to my beloved wife Jie Li, and to my parents Cai Yao and Hexiang Liu for their unconditional support. This thesis is also dedicated to Saber, Artoria Pendragon, who always inspires me with her strong will and noble spirit. ii Acknowledgements First I want to thank my mentor, Dr. Daniel J. Klionsky, for his continuous support and patient guidance during my Ph.D. works. Dan is a great scientist as well as a wise advisor. His passion in science and helpful advice on my projects always encouraged me to plan ahead and consider potential problems before they develop. Five years’ experience in one’s 20s will greatly shape his view in both career and life, and I feel so lucky to have Dan as my example during my graduate life. I also want to thank my thesis committee members, Professor Haoxing Xu, Professor Lois S. Weisman and Professor Laura Olsen. Your generous support and immense knowledge provided me with invaluable suggestions and criticisms for my research. Without all this help, I could not finish this thesis. Here I would like to express my sincere thanks for all of the efforts you made.
    [Show full text]