20q amplification defined by genomic and clinical characteristics as a subgroup with increased prevalence and better survival in metastatic colorectal cancer.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e16003-e16003
Author(s):  
Satish Maharaj ◽  
RuoBing Xue ◽  
Anmol Cheema
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Survival Data ◽  
Information Exchange ◽  
Clinical Characteristics ◽  
The Cancer Genome Atlas ◽  
Independent Prognostic Marker ◽  
Cancer Genome Atlas ◽  
Microsatellite Stability ◽  
Next Generation Sequencing Ngs

e16003 Background: Genomic instability from 20q amplification is an oncogenic pathway in colorectal cancer (CRC). Several genes have been implicated, including BCL2L1, AURKA, SRC, ASXL1, GNAS and TOP1. There is a lack of data regarding 20q amplified group and one study implicating these genes suggested these patients have better overall survival. Next Generation Sequencing (NGS) has become widely used in metastatic CRC (mCRC) and easily identifies patients with 20q amplification. Nevertheless, most oncologists do not routinely consider 20q amplification status and this subgroup remains underinvestigated. This study aims to investigate genomic and clinical characteristics of 20q amplified mCRC using a single-center retrospective cohort and a multi-center genomic dataset. Methods: A cohort was identified comprising patients with mCRC who had NGS testing of tumor DNA and were treated between 2014-2019. Cases with and without 20q amplification were identified. Genomic, clinical and survival data were analyzed. Significant genomic findings were compared with all-stage CRC data using the AACR Genomic Evidence Neoplasia Information Exchange (GENIE) and The Cancer Genome Atlas (TCGA) databases. Results: Of the mCRC cohort ( n= 72), 15% ( n= 11) had 20q amplification. Amplified and non-amplified groups had no significant differences in age, sex or follow-up time. Patients with 20q amplification were more likely to have never smoked, and less likely to have treatment with targeted therapy. Survival analysis showed clear separation with longer overall survival for the amplified group. Eight genes at loci 20q11 to 20q13 were amplified - in order of frequency: ASXL1, GNAS, ARFRP1, ZNF217, AURKA, BCL2L1, SRC and TOP1. 20q amplification was significantly associated with wild-type RAS and BRAF, microsatellite stability, mutant TP53 and mutant APC. Using the GENIE and TCGA databases, it was found that metastatic disease had increased prevalence of all 20q amplified genes except TOP1, when compared to all-stage CRC. Conclusions: Clinical use of NGS identifies the 20q amplification subgroup that has increased prevalence in mCRC (compared to all CRC). Compared to non-20q amplified mCRC, this group had better survival, suggesting genomic pattern in mCRC is a novel independent prognostic marker. We believe mCRC patients would benefit from further studies defining a genomic prognostication model and development of therapy targeting the 20q amplification pathway.

scholarly journals Predicted CD4+ T cell infiltration levels could indicate better overall survival in sarcoma patients

2021 ◽  
Vol 49 (1) ◽  
pp. 030006052098153
Author(s):  
Qing Bi ◽  
Yang Liu ◽  
Tao Yuan ◽  
Huizhen Wang ◽  
Bin Li ◽  
...  
Keyword(s):  
Overall Survival ◽  
T Cell ◽  
Survival Data ◽  
Tumor Infiltrating Lymphocytes ◽  
The Cancer Genome Atlas ◽  
Cell Infiltration ◽  
T Cell Infiltration ◽  
Whole Exome ◽  
Cancer Genome Atlas ◽  
Infiltrating Lymphocytes

Objective The role of tumor-infiltrating lymphocytes (TILs) has not yet been characterized in sarcomas. The aim of this bioinformatics study was to explore the effect of TILs on sarcoma survival and genome alterations. Methods Whole-exome sequencing, transcriptome sequencing, and survival data of sarcoma were obtained from The Cancer Genome Atlas. Immune infiltration scores were calculated using the Tumor Immune Estimation Resource. Potential associations between abundance of infiltrating TILs and survival or genome alterations were examined. Results Levels of CD4+ T cell infiltration were associated with overall survival of patients with pan-sarcomas, and higher CD4+ T cell infiltration levels were associated with better survival. Somatic copy number alterations, rather than mutations, were found to correlate with CD4+ T cell infiltration levels. Conclusions This data mining study indicated that CD4+ T cell infiltration levels predicted from RNA sequencing could predict sarcoma prognosis, and higher levels of CD4+ T cells infiltration indicated a better chance of survival.

Identification of a lncRNA prognostic signature-related to stem cell index and its significance in colorectal cancer

2021 ◽  
Author(s):  
Xiao-Cheng Wang ◽  
Ya Liu ◽  
Fei-Wu Long ◽  
Liang-Ren Liu ◽  
Chuan-Wen Fan
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Prognostic Markers ◽  
The Cancer Genome Atlas ◽  
Prognostic Signature ◽  
Free Survival ◽  
Cancer Genome Atlas ◽  
Bioinformatic Approaches ◽  
Cell Phenotypes ◽  
The Relationship

Background: The relationship between long noncoding RNAs (lncRNAs) and the mRNA stemness index (mRNAsi) in colorectal cancer (CRC) is still unclear. Materials & methods: The mRNAsi, mRNAsi-related lncRNAs and their clinical significance were analyzed by bioinformatic approaches in The Cancer Genome Atlas (TCGA)-COREAD dataset. Results: mRNAsi was negatively related to pathological features but positively related to overall survival and recurrence-free survival in CRC. A five mRNAsi-related lncRNAs prognostic signature was further developed and showed independent prognostic factors related to overall survival in CRC patients, due to the five mRNAsi-related lncRNAs involved in several pathways of the cancer stem cells and malignant cancer cell phenotypes. Conclusion: The present study highlights the potential roles of mRNAsi-related lncRNAs as alternative prognostic markers.

scholarly journals Identification of novel alternative splicing isoform biomarkers and their association with overall survival in colorectal cancer

2019 ◽  
Author(s):  
Hongtao Jia ◽  
Aili Wang ◽  
Haifeng Lian ◽  
Yuanyuan Shen ◽  
Qian Wang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Alternative Splicing ◽  
Cancer Biology ◽  
The Cancer Genome Atlas ◽  
Normal Tissues ◽  
Eukaryotic Gene ◽  
Cancer Genome Atlas ◽  
Alternative Splicing Events ◽  
Therapeutic Tools

Abstract Alternative splicing is an important mechanism of regulating eukaryotic gene expression. Understanding the most common alternative splicing events in colorectal cancer (CRC) will help developing diagnostic, prognostic or therapeutic tools in CRC. Publicly available RNA-seq data of 31 pairs of CRC and normal tissues and 18 pairs of metastatic and normal tissues were used to identify alternative splicing events using PSI and DEXSeq methods. The highly significant splicing events were used to search a database of The Cancer Genome Atlas (TCGA). We identified alternative splicing events in 10 genes marking the signature of CRC (more inclusion of CLK1-E4, COL6A3-E6, CD44v8-10, alternative first exon regulation of ARHGEF9, CHEK1, HKDC1 and HNF4A) or metastasis (decrease of SERPINA1-E1a, CALD-E5b, E6 and FBLN2-E9). Except for CHEK1, all other 9 splicing events were confirmed by TCGA data with 382 CRC tumors and 52 normal controls. Two splicing events (COL6A3 and HKDC1) were found to be significantly associated with patient overall survival. The alternative splicing signatures of the 10 genes are highly consistent with previous reports and/or relevant to cancer biology. The significant association of higher expression of the COL6A3 E5-E6 junction and HKDC1 E1-E2 with better overall survival was firstly reported. This study might be of significant value in the future biomarker, prognosis marker and therapeutics development of CRC.

scholarly journals Angiogenin Upregulation Independently Predicts Unfavorable Overall Survival in Proneural Subtype of Glioblastoma

2019 ◽  
Vol 18 ◽  
pp. 153303381984663
Author(s):  
Ji-liang Hu ◽  
Wei-Jian Luo ◽  
Hao Wang
Keyword(s):  
Overall Survival ◽  
Survival Data ◽  
Cox Regression ◽  
The Cancer Genome Atlas ◽  
Isocitrate Dehydrogenase 1 ◽  
Study Results ◽  
Cancer Genome Atlas ◽  
Secondary Study ◽  
Independent Indicator ◽  
Temozolomide Chemotherapy

Objective: Angiogenin is a small protein that exerts potent stimulating effects on angiogenesis. In this study, we aimed to examine the expression of angiogenin in different subtypes of glioblastoma and estimated its independent prognostic value. Methods: The genomic and survival data from The Cancer Genome Atlas-glioblastoma were extracted for a secondary study. Results The expression of angiogenin was upregulated in glioblastoma tissues and varied significantly in different subtypes. Although the proneural subtype had the lowest angiogenin expression, high angiogenin expression was associated with significantly worse overall survival. However, this association was not observed in other subtypes. By performing univariate and multivariate analysis using Cox regression model, we observed that high angiogenin expression was an independent indicator of shorter overall survival in proneural glioblastoma (hazard ratio: 1.669, 95% confidence interval: 1.033-2.696, P = .036), after adjustment of age, gender, isocitrate dehydrogenase 1 mutation, temozolomide chemotherapy and radiation therapy. In addition, we also observed a correlation between elevated angiogenin expression and the hypomethylated status of its DNA. The hypermethylation group had significantly better overall survival. Conclusions: Angiogenin upregulation might serve as a biomarker for unfavorable overall survival in the proneural subtype of glioblastoma.

scholarly journals Identification of lnc RNAs Related to Prognosis of Patients With Colorectal Cancer

2020 ◽  
Vol 19 ◽  
pp. 153303382096212
Author(s):  
Yuqi Sun ◽  
Peng Peng ◽  
Lanlan He ◽  
Xueren Gao
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Cox Regression ◽  
The Cancer Genome Atlas ◽  
High Expression ◽  
Cox Regression Analysis ◽  
Cancer Genome Atlas ◽  
Score Model ◽  
Prognostic Prediction

The purpose of this study was to identify long noncoding RNAs (lncRNAs) related to prognosis of patients with colorectal cancer (CRC) and develop a prognostic prediction model for CRC. Transcriptome data and survival information of CRC patients were downloaded from The Cancer Genome Atlas. The differentially expressed lncRNAs (DElncRNAs) between CRC and normal colorectal tissues were identified by the edgeR package. The association of DElncRNAs expression with prognosis of CRC patients was analyzed by the survival package. A nomogram predicting 3- and 5- year overall survival of CRC patients was drawn by the rms package. A total of 1046 DElncRNAs were identified, including 271 down-regulated and 775 up-regulated lncRNAs in CRC. Multivariate Cox regression analysis showed 10 lncRNAs related to the prognosis of CRC patients. Thereinto high expression of AC004009.1, LHX1-DT, ELFN1-AS1, AL136307.1, AC087379.2, RBAKDN and AC078820.1 was associated with poorer prognosis of CRC patients. High expression of LINC01055, AL590483.1 and AC008514.1 was associated with better prognosis of CRC patients. Furthermore, the risk score model developed based on the 10 lncRNAs could effectively predict overall survival of CRC patients. In conclusion, 10 prognostic biomarkers for CRC were identified, which would be helpful to understand the role of lncRNAs in CRC progression.

scholarly journals Identification of Hub Genes for Controlling Cancer Stem Cell Characteristics in Colorectal Cancer by Bioinformatics Analysis

2021 ◽  
Author(s):  
Xiang Li ◽  
Shuoyang Huang ◽  
Chao Yang ◽  
Yongbin Zheng
Keyword(s):  
Colorectal Cancer ◽  
Stem Cell ◽  
Survival Data ◽  
Prognostic Model ◽  
The Cancer Genome Atlas ◽  
Lasso Regression ◽  
Immune Microenvironment ◽  
Hub Genes ◽  
Normal Tissues ◽  
Cancer Genome Atlas

Abstract Background Cancer stem cells (CSCs), which are capable of infinite proliferation and self-renewal, play a crucial role in the occurrence and development of colorectal cancer (CRC). The study of the expression characteristics of CRC stem cell-related genes and their interaction with the immune microenvironment may contribute to CRC treatment. Results In order to explore the hub genes that regulate the stemness characteristics of CRC, we obtained gene expression values of the Cancer Genome Atlas (TCGA), stemness indices (mRNAsi), and corresponding survival data from UCSC Xena Browser. Differentially expressed genes (DEGs) were identified in cancer and normal tissues. Then we screened 2 modules and 210 mRNAsi-related genes from 4,941 DEGs by weighted gene co-expression network analysis. A prognostic model including ten genes (VCAN, SPARC, COL12A1, THBS2, COL1A2, COL5A1, TAGLN, DCN, MYH11, CDH11) was constructed using protein interaction networks and LASSO regression. We also evaluated the relationship between cancer stemness and immune response and found there was a strong correlation between each other. Conclusions Our study establishes a prognostic model associated with CSCs and reveals the association between mRNAsi and the tumor immune microenvironment, which is useful for the targeted therapy of CRC.

scholarly journals Identification KCNE4 and DNASE1L3 for Prognostic Utility in Colorectal Cancer: A Bioinformatics Analysis

2021 ◽  
Author(s):  
Deming Liu ◽  
Xue Xiang ◽  
Yaqiong Chen ◽  
Yajun Jiao ◽  
Liuli Wang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Survival Prognosis ◽  
Online Databases ◽  
Prognostic Utility ◽  
Cancer Genome Atlas ◽  
Advanced Stages ◽  
Using Data ◽  
Microsatellite Stability

Abstract Objective: Immunotherapy has improved the prognosis of cancer patients who did not benefit from conventional treatment and decreased mortality, which has become an effective treatment for multiple carcinomas in their advanced stages. Patients with colorectal cancer (CRC) were mostly in the state of mismatch repair-proficient or microsatellite stability, with limited benefit in immunotherapy. Hence, immunotherapy strategies for CRC still need to be explored continuously. Methods: Based on comprehensive analysis of the immune infiltration associated genes in the Cancer Genome Atlas (TCGA) database and differential genes for the progression and metastasis of CRC in the Gene Expression Omnibus (GEO) database, as well as validation analysis on several online databases, we obtained two genes (KCNE4 and DNASE1L3) as novel immune-related molecules for CRC. Results: High expression of KCNE4 and DNASE1L3 were significantly correlated with CRC progression and prognosis, and were strongly associated with the infiltration of different types of macrophages in the CRC tumor microenvironment. In addition, we analysed the guidance value of KCNE4 and DNASE1L3 in anti-PD-1 therapy using data from the IMvigor210 group, and predicted the significant value of KCNE4 and DNASE1L3 in CRC immunotherapy by analyzing the correlation of KCNE4 and DNASE1L3 with the expression of CRC immune checkpoint markers. Conclusions: We hypothesized that DNASE1L3 and KCNE4 would be potential prognostic biomarkers and predictors of immunotherapy in CRC. Our results may serve as an indication of survival prognosis and provide a new assessment indicator for the choice of immunotherapy for CRC patients.

scholarly journals Identification of novel alternative splicing isoform biomarkers and their association with overall survival in colorectal cancer

2019 ◽  
Author(s):  
Haifeng Lian ◽  
Aili Wang ◽  
Yuanyuan Shen ◽  
Qian Wang ◽  
Zhenru Zhou ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Alternative Splicing ◽  
Cancer Biology ◽  
The Cancer Genome Atlas ◽  
Normal Tissues ◽  
Eukaryotic Gene ◽  
Cancer Genome Atlas ◽  
Alternative Splicing Events ◽  
Therapeutic Tools

Abstract Alternative splicing is an important mechanism of regulating eukaryotic gene expression. Understanding the most common alternative splicing events in colorectal cancer (CRC) will help developing diagnostic, prognostic or therapeutic tools in CRC. Publicly available RNA-seq data of 31 pairs of CRC and normal tissues and 18 pairs of metastatic and normal tissues were used to identify alternative splicing events using PSI and DEXSeq methods. The highly significant splicing events were used to search a database of The Cancer Genome Atlas (TCGA). We identified alternative splicing events in 10 genes marking the signature of CRC (more inclusion of CLK1-E4, COL6A3-E6, CD44v8-10, alternative first exon regulation of ARHGEF9, CHEK1, HKDC1 and HNF4A) or metastasis (decrease of SERPINA1-E1a, CALD-E5b, E6 and FBLN2-E9). Except for CHEK1, all other 9 splicing events were confirmed by TCGA data with 382 CRC tumors and 52 normal controls. Two splicing events (COL6A3 and HKDC1) were found to be significantly associated with patient overall survival. The alternative splicing signatures of the 10 genes are highly consistent with previous reports and/or relevant to cancer biology. The significant association of higher expression of the COL6A3 E5-E6 junction and HKDC1 E1-E2 with better overall survival was firstly reported. This study might be of significant value in the future biomarker, prognosis marker and therapeutics development of CRC.

scholarly journals Identification of novel alternative splicing isoform biomarkers and their association with overall survival in colorectal cancer

2020 ◽  
Author(s):  
Haifeng Lian ◽  
Aili Wang ◽  
Yuanyuan Shen ◽  
Qian Wang ◽  
Zhenru Zhou ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Alternative Splicing ◽  
Cancer Biology ◽  
The Cancer Genome Atlas ◽  
Sample Type ◽  
Normal Tissues ◽  
Eukaryotic Gene ◽  
Cancer Genome Atlas ◽  
Therapeutic Tools

Abstract Background: Alternative splicing (AS) is an important mechanism of regulating eukaryotic gene expression. Understanding the most common AS events in colorectal cancer (CRC) will help developing diagnostic, prognostic or therapeutic tools in CRC.Methods: Publicly available RNA-seq data of 28 pairs of CRC and normal tissues and 18 pairs of metastatic and normal tissues were used to identify AS events using PSI and DEXSeq methods. Result: The highly significant splicing events were used to search a database of The Cancer Genome Atlas (TCGA). We identified AS events in 9 genes in CRC (more inclusion of CLK1-E4, COL6A3-E6, CD44v8-10, alternative first exon regulation of ARHGEF9, CHEK1, HKDC1 and HNF4A) or metastasis (decrease of SERPINA1-E1a, CALD-E5b, E6). Except for CHEK1, all other 8 splicing events were confirmed by TCGA data with 382 CRC tumors and 51 normal controls. The combination of three splicing events was used to build a logistic regression model that can predict sample type (CRC or normal) with near perfect performance (AUC=1). Two splicing events (COL6A3 and HKDC1) were found to be significantly associated with patient overall survival. The AS features of the 9 genes are highly consistent with previous reports and/or relevant to cancer biology. Conclusions: The significant association of higher expression of the COL6A3 E5-E6 junction and HKDC1 E1-E2 with better overall survival was firstly reported. This study might be of significant value in the future biomarker, prognosis marker and therapeutics development of CRC.

scholarly journals Identification of novel alternative splicing isoform biomarkers and their association with overall survival in colorectal cancer

2020 ◽  
Author(s):  
Haifeng Lian ◽  
Aili Wang ◽  
Yuanyuan Shen ◽  
Qian Wang ◽  
Zhenru Zhou ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Alternative Splicing ◽  
Cancer Biology ◽  
The Cancer Genome Atlas ◽  
Sample Type ◽  
Normal Tissues ◽  
Eukaryotic Gene ◽  
Cancer Genome Atlas ◽  
Therapeutic Tools

Abstract Background: Alternative splicing (AS) is an important mechanism of regulating eukaryotic gene expression. Understanding the most common AS events in colorectal cancer (CRC) will help developing diagnostic, prognostic or therapeutic tools in CRC.Methods: Publicly available RNA-seq data of 28 pairs of CRC and normal tissues and 18 pairs of metastatic and normal tissues were used to identify AS events using PSI and DEXSeq methods. Result: The highly significant splicing events were used to search a database of The Cancer Genome Atlas (TCGA). We identified AS events in 9 genes in CRC (more inclusion of CLK1-E4, COL6A3-E6, CD44v8-10, alternative first exon regulation of ARHGEF9, CHEK1, HKDC1 and HNF4A) or metastasis (decrease of SERPINA1-E1a, CALD-E5b, E6). Except for CHEK1, all other 8 splicing events were confirmed by TCGA data with 382 CRC tumors and 51 normal controls. The combination of three splicing events was used to build a logistic regression model that can predict sample type (CRC or normal) with near perfect performance (AUC=1). Two splicing events (COL6A3 and HKDC1) were found to be significantly associated with patient overall survival. The AS features of the 9 genes are highly consistent with previous reports and/or relevant to cancer biology. Conclusions: The significant association of higher expression of the COL6A3 E5-E6 junction and HKDC1 E1-E2 with better overall survival was firstly reported. This study might be of significant value in the future biomarker, prognosis marker and therapeutics development of CRC.

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