Establishment of the prognostic index of lung squamous cell carcinoma based on immunogenomic landscape analysis

Cancer Cell International
Jianguo ZhangConghua Xie

Abstract

The incidence of lung squamous cell carcinoma (LUSC) increased substantially in recent years. Systematical investigation of the immunogenomic pattern is critical to improve the prognosis of LUSC. Based on the TCGA and GEO dataset, we integrated the immune-related genes (IRGs) expression profile and the overall survival (OS) of 502 patients with LUSC. The survival-related and differentially-expressed IRGs in LUSC patients were evaluated by univariate cox regression and LASSO regression analysis. By applying multivariate cox analysis, a new prognostic indicator based on IRGs was established. We also used CIBERSORT algorithms and TIMER database to analyze immune infiltration of LUSC. Both gene set enrichment analysis (GSEA) and principal component analysis (PCA) was carried out for functional annotation. With the assist of computational biology, we also investigated the latent properties and molecular mechanisms of these LUSC-specific IRGs. We analyzed the correlation between immune checkpoints and risk score. A novel prognostic model was established based on 11 IRGS, including CXCL5, MMP12, PLAU, ELN, JUN, RNASE7, JAG1, SPP1, AGTR2, FGFR4, and TNFRSF18. This model performed well in the prognostic forecast, and was also related to...Continue Reading

References

Mar 1, 1994·Radiographics : a Review Publication of the Radiological Society of North America, Inc·M L Rosado-de-ChristensonC A Moran
Dec 6, 2008·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Fred R HirschMauro Papotti
Mar 16, 2012·Nature Reviews. Cancer·Wolf Herman FridmanJérôme Galon
Dec 1, 2012·Archives of Pathology & Laboratory Medicine·Larry NicholsFriedrich D Knollmann
Apr 4, 2013·Science Signaling·Jianjiong GaoNikolaus Schultz
Feb 7, 2014·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·Oksana KowalczukJacek Niklinski
May 6, 2014·Immunologic Research·Sanchita BhattacharyaAtul J Butte
Feb 11, 2015·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Dirk SchadendorfJedd D Wolchok
Apr 4, 2015·Science·Ton N Schumacher, Robert D Schreiber
Apr 14, 2015·British Journal of Cancer·K MavridisA Scorilas
Aug 21, 2015·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·William D TravisUNKNOWN WHO Panel
Dec 4, 2015·Drug Discoveries & Therapeutics·Shuzhan LiXiubao Ren
Jul 22, 2016·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Kurt A SchalperDavid L Rimm
Oct 16, 2016·Journal of the National Cancer Institute·Rico D BenseRudolf S N Fehrmann
Jan 7, 2017·Current Opinion in Oncology·Jordi Remon, Benjamin Besse
Aug 9, 2017·Journal of Thoracic Imaging·Brett W CarterPatricia M de Groot
Aug 22, 2017·Biomedicine & Pharmacotherapy = Biomédecine & Pharmacothérapie·Xinyan LiuZhihua Hou
Aug 30, 2017·Cancer Immunology Research·Tullia C BrunoJill E Slansky
Sep 8, 2017·Open Biology·Sean Blandin KnightCaroline Dive
Nov 3, 2017·Cancer Research·Shenglin MeiX Shirley Liu
Dec 6, 2017·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Franz Villarroel-EspindolaKurt A Schalper
Feb 13, 2018·The Journal of Thoracic and Cardiovascular Surgery·Ezra EllaOri Wald
Mar 14, 2018·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Kimio YonesakaKazuhiko Nakagawa
Aug 2, 2018·The Journal of Clinical Investigation·Aleksandra PopovicNeeha Zaidi
Dec 18, 2018·Expert Opinion on Therapeutic Targets·Ghasem GhalamfarsaFarhad Jadidi-Niaragh
Jan 9, 2019·CA: a Cancer Journal for Clinicians·Rebecca L SiegelAhmedin Jemal
May 6, 2019·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Ila DatarKurt A Schalper
May 12, 2019·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Tokiyoshi TanegashimaHiroyoshi Nishikawa
Sep 14, 2019·Cancer Cell International·Liwei WangZhiwen Chen
Nov 19, 2019·Open Medicine·Changgong Zhang, Xuezhi Hao

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-seq
PCA
methylation profiling

Software Mentioned

org
Hs
CIBERSORT
GSEA
R
GOplot
limma
glmnet
clusterProfiler
survminer

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.