High-risk, Expression-Based Prognostic Long Noncoding RNA Signature in Neuroblastoma

JNCI Cancer Spectrum
Divya SahuHsuan-Cheng Huang

Abstract

Current clinical risk factors stratify patients with neuroblastoma (NB) for appropriate treatments, yet patients with similar clinical behaviors evoke variable responses. MYCN amplification is one of the established drivers of NB and, when combined with high-risk displays, worsens outcomes. Growing high-throughput transcriptomics studies suggest long noncoding RNA (lncRNA) dysregulation in cancers, including NB. However, expression-based lncRNA signatures are altered by MYCN amplification, which is associated with high-risk, and patient prognosis remains limited. We investigated RNA-seq-based expression profiles of lncRNAs in MYCN status and risk status in a discovery cohort (n = 493) and validated them in three independent cohorts. In the discovery cohort, a prognostic association of lncRNAs was determined by univariate Cox regression and integrated into a signature using the risk score method. A novel risk score threshold selection criterion was developed to stratify patients into risk groups. Outcomes by risk group and clinical subgroup were assessed using Kaplan-Meier survival curves and multivariable Cox regression. The performance of lncRNA signatures was evaluated by receiver operating characteristic curve. All statistic...Continue Reading

References

Oct 31, 1985·The New England Journal of Medicine·R C SeegerD Hammond
Aug 1, 1993·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·G M BrodeurF Hedborg
Nov 5, 1997·Journal of Pediatric Hematology/oncology·J G GurneyL L Robison
Nov 24, 1999·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·J M Maris, K K Matthay
Mar 4, 2003·Nature Reviews. Cancer·Garrett M Brodeur
Jun 20, 2003·European Urology·Daphne HesselsJack A Schalken
Aug 24, 2005·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·W B LondonS L Cohn
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Sep 7, 2006·Journal of the National Cancer Institute·Shahab AsgharzadehRobert C Seeger
Jun 26, 2007·Lancet·John M MarisSusan L Cohn
Aug 27, 2009·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Jun S WeiJaved Khan
Feb 25, 2010·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Katleen De PreterJo Vandesompele
May 18, 2010·International Journal of Cancer. Journal International Du Cancer·Johannes H SchulteAlexander Schramm
Jun 19, 2010·The New England Journal of Medicine·John M Maris
Mar 19, 2011·BMC Bioinformatics·Xavier RobinMarkus Müller
Apr 16, 2011·Cancer Cell International·Frida AbelStaffan Nilsson
Oct 28, 2011·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Katleen De PreterJo Vandesompele
Jun 6, 2012·Annual Review of Biochemistry·John L Rinn, Howard Y Chang
Aug 29, 2012·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Shahab AsgharzadehRobert C Seeger
Oct 9, 2012·Nature Genetics·Jan J MolenaarJohannes H Schulte
Oct 24, 2012·Proceedings of the National Academy of Sciences of the United States of America·Linda J ValentijnRogier Versteeg
Oct 3, 2013·Cold Spring Harbor Perspectives in Medicine·Miller Huang, William A Weiss
Jun 8, 2014·Journal of the National Cancer Institute·Pei Y LiuTao Liu
Jul 16, 2014·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·Bin CaiSen Zhang
Nov 19, 2014·International Journal of Oncology·Hee Jung KimYoung Tae Kim
Jan 20, 2015·Nature Genetics·Matthew K IyerArul M Chinnaiyan
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
May 13, 2015·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Sheng-xian YuanWei-ping Zhou
Jun 19, 2015·Oncotarget·Gaurav Kumar Pandey, Chandrasekhar Kanduri
Jun 24, 2015·Cancer Research·Mike R RussellKristina A Cole
Dec 2, 2015·Oncology Letters·Jing-Bo ShaoHui Jiang
Jan 16, 2016·Proceedings of the National Academy of Sciences of the United States of America·Kenzui TaniueTetsu Akiyama

❮ Previous
Next ❯

Citations

Dec 24, 2019·Frontiers in Oncology·Jian-Guo ZhouUdo S Gaipl
Sep 10, 2020·Cancer Management and Research·Yanping HuXiaomin Zhang
Oct 17, 2019·Frontiers in Genetics·Christopher M SmithGyorgy Hutvagner
Dec 10, 2020·Cancer Cell International·Shengyang GeChuanyu Sun

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE62564
GSE16476
50

Methods Mentioned

BETA
RNA-seq
ChIP-seq

Software Mentioned

Gencode
Enrichment map -
pROC R
limma R
Cytoscape
GSEA

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.