Development of a Machine Learning-Based Autophagy-Related lncRNA Signature to Improve Prognosis Prediction in Osteosarcoma Patients.

Frontiers in Molecular Biosciences
Guangzhi ZhangQi-Qi Xie

Abstract

Osteosarcoma is a frequent bone malignancy in children and young adults. Despite the availability of some prognostic biomarkers, most of them fail to accurately predict prognosis in osteosarcoma patients. In this study, we used bioinformatics tools and machine learning algorithms to establish an autophagy-related long non-coding RNA (lncRNA) signature to predict the prognosis of osteosarcoma patients. We obtained expression and clinical data from osteosarcoma patients in the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Gene Expression Omnibus (GEO) databases. We acquired an autophagy gene list from the Human Autophagy Database (HADb) and identified autophagy-related lncRNAs by co-expression analyses. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the autophagy-related lncRNAs were conducted. Univariate and multivariate Cox regression analyses were performed to assess the prognostic value of the autophagy-related lncRNA signature and validate the relationship between the signature and osteosarcoma patient survival in an independent cohort. We also investigated the relationship between the signature and immune cell infiltration. We initiall...Continue Reading

References

Mar 1, 1987·RöFo : Fortschritte auf dem Gebiete der Röntgenstrahlen und der Nuklearmedizin·M NadjmiB Schuknecht
May 1, 1995·Journal of Bone and Mineral Research : the Official Journal of the American Society for Bone and Mineral Research·J G Meszaros, N J Karin
Aug 30, 2003·Immunology Letters·Jolanta ArtymMarian L Kruzel
Mar 8, 2008·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Alexia IasonosKatherine S Panageas
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Nov 30, 2012·Nucleic Acids Research·Tanya BarrettAlexandra Soboleva
Jan 18, 2013·BMC Bioinformatics·Sonja HänzelmannJustin Guinney
Nov 2, 2013·Asian Pacific Journal of Cancer Prevention : APJCP·Jian LiYu Guo
Oct 1, 2015·Biomedicine & Pharmacotherapy = Biomédecine & Pharmacothérapie·Zhen YangXiaoke Sun
Jun 4, 2016·International Immunopharmacology·Sheng-Dong WangZhao-Ming Ye
Mar 7, 2017·Journal of Adolescent and Young Adult Oncology·Fergal C Kelleher, Hazel O'Sullivan
May 26, 2017·Current Opinion in Pharmacology·Nathalie DehneBernhard Brüne
Jul 29, 2017·Nature Reviews. Cancer·Jean M Mulcahy LevyAndrew Thorburn
Sep 4, 2017·Life Sciences·Palaniyandi RavananPriti Talwar
Sep 28, 2017·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Zhiqiang ZhaoJingnan Shen
Nov 10, 2017·Cellular Immunology·Marie-Françoise HeymannDominique Heymann
Jan 19, 2018·Methods in Molecular Biology·Binbin ChenAsh A Alizadeh
Feb 13, 2018·BMB Reports·Sarala Manandhar, You Mie Lee
Jun 21, 2018·Pediatric Blood & Cancer·Mary F WedekindTimothy P Cripe
Jun 29, 2018·Breast Care·André Steven, Barbara Seliger
Jul 5, 2018·Journal of Experimental & Clinical Cancer Research : CR·Fan ZhangTingting Ren
Sep 9, 2018·Osteoporosis International : a Journal Established As Result of Cooperation Between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA·E Canalis
Oct 3, 2018·Cancer Chemotherapy and Pharmacology·Dumnoensun PruksakornChantragan Srisomsap
Oct 12, 2018·Medicinal Research Reviews·Hendrik FolkertsValerie R Wiersma
Jan 12, 2019·Cell·Beth Levine, Guido Kroemer
Feb 23, 2019·International Journal of Immunopathology and Pharmacology·Jun ChenYong Zhang
May 31, 2019·Human Genetics·Shi Q WongLouis R Lapierre
Jun 27, 2019·The Journal of Pathology·Gian Luca NegriPoul H Sorensen
Aug 23, 2019·Cancer Discovery·Ravi K AmaravadiJayanta Debnath
Aug 27, 2019·Expert Review of Molecular Diagnostics·Rachel Sin-Yu ChoiSze Chuen Cesar Wong
Sep 5, 2019·Cells·Yujing ChiJichun Yang
Sep 27, 2019·Journal of Cellular and Molecular Medicine·Zhiwang SongChunyan Dong

❮ Previous
Next ❯

Software Mentioned

all
clusterProfiler
glmnet
CIBERSORT
limma
GSEA
R package “ survivalROC ”
clusterProfiler package
ggplot2 package x
R package

Related Concepts

Related Feeds

Cancer Biology: Molecular Imaging

Molecular imaging enables noninvasive imaging of key molecules that are crucial to tumor biology. Discover the latest research in molecular imaging in cancer biology in this feed.

Autophagy & Disease

Autophagy is an important cellular process for normal physiology and both elevated and decreased levels of autophagy are associated with disease. Here is the latest research.

Parkinson's Disease & Autophagy (MDS)

Autophagy leads to degradation of damaged proteins and organelles by the lysosome. Impaired autophagy has been implicated in several diseases. Here is the role of autophagy in Parkinson’s disease.

Cancer Vaccines

Cancer vaccines are vaccines that either treat existing cancer or prevent development of a cancer.

Autophagy & Metabolism

Autophagy preserves the health of cells and tissues by replacing outdated and damaged cellular components with fresh ones. In starvation, it provides an internal source of nutrients for energy generation and, thus, survival. A powerful promoter of metabolic homeostasis at both the cellular and whole-animal level, autophagy prevents degenerative diseases. It does have a downside, however--cancer cells exploit it to survive in nutrient-poor tumors.

Autophagy & Model Organisms

Autophagy is a cellular process that allows degradation by the lysosome of cytoplasmic components such as proteins or organelles. Here is the latest research on autophagy & model organisms