scholarly journals Expression and Prognostic Characteristics of Ferroptosis-Related Genes in Colon Cancer

2021 ◽  
Vol 22 (11) ◽  
pp. 5652
Author(s):  
Jie Zhu ◽  
Weikaixin Kong ◽  
Zhengwei Xie
Keyword(s):  
Colon Cancer ◽  
The Cancer Genome Atlas ◽  
Braf Mutations ◽  
Mutation Burden ◽  
The Status ◽  
Prognosis Model ◽  
Cancer Genome Atlas ◽  
Causes Of Mortality ◽  
New Type ◽  
Checkpoint Genes

Ferroptosis is a new type of programmed cell death, which occurs with iron dependence. Previous studies have showed that ferroptosis plays an important regulatory role in the occurrence and development of tumors. Colon cancer is one of the major morbidities and causes of mortality in the world. This study used RNA-seq and colon cancer clinical data to explore the relationship between ferroptosis-related genes and colon cancer. Based on the fifteen prognostic ferroptosis-related genes, two molecular subgroups of colon cancer were identified. Surprisingly, we also found cluster2 was characterized by lower mutation burden and expression of checkpoint genes, better survival, and higher expression of NOX1. Moreover, cluster2 has fewer BRAF mutations. We also found the expression of NOX1 is related to the status of BRAF. Finally, using 15 ferroptosis-related genes from The Cancer Genome Atlas cohort, we constructed a prognosis model, and this model may be used to predict the prognosis of patients in clinics.

scholarly journals Expression and Prognostic Characteristics of m6A RNA Methylation Regulators in Colon Cancer

2021 ◽  
Vol 22 (4) ◽  
pp. 2134
Author(s):  
Liting Huang ◽  
Jie Zhu ◽  
Weikaixin Kong ◽  
Peifeng Li ◽  
Sujie Zhu
Keyword(s):  
Colon Cancer ◽  
Clinical Information ◽  
The Cancer Genome Atlas ◽  
Cancer Cell Proliferation ◽  
Genetic Changes ◽  
Prognosis Model ◽  
Cancer Genome Atlas ◽  
M6a Rna Methylation ◽  
The Relationship

Colon cancer is a common and leading cause of death and malignancy worldwide. N6-methylation of adenosine (m6A) is the most common reversible mRNA modification in eukaryotes, and it plays a crucial role in various biological functions in vivo. Dysregulated expression and genetic changes of m6A regulators have been correlated with tumorigenesis, cancer cell proliferation, tumor microenvironment, and prognosis in cancers. This study used RNA-seq and colon cancer clinical data to explore the relationship between N6-methylation and colon cancer. Based on the seven m6A regulators related to prognosis, three molecular subgroups of colon cancer were identified. Surprisingly, we found that each subgroup had unique survival characteristics. We then identified three subtypes of tumors based on 299 m6A phenotype-related genes, and one subtype was characterized as an immunosuppressive tumor and patients in this subtype may be more suitable for immunotherapy than other subtypes. Finally, using m6A-related genes and clinical information from The Cancer Genome Atlas cohort, we constructed a prognosis model, and this model could be used to predict the prognosis of patients in clinics.

scholarly journals Development of Prognostic Model Based on Five-gene Related to Tumor Mutation Burden in Hepatocellular Carcinoma

2021 ◽  
Author(s):  
Zhou Shujun ◽  
Qingling Li ◽  
Bin Yu ◽  
Qifa Ye ◽  
Yanfeng Wang
Keyword(s):  
The Cancer Genome Atlas ◽  
Missense Mutations ◽  
Tumor Mutation Burden ◽  
Mutation Burden ◽  
Prognosis Model ◽  
Cancer Genome Atlas ◽  
Matrix Organization ◽  
The Individual ◽  
Therapeutic Decision Making ◽  
High Level

Abstract BackgroundHepatocellular carcinoma (HCC) , the incidence rate ranks sixth and regards as the second leading cause of cancer-related death in the world. Tumor mutation burden (TMB) , a novel biomarker featured with microsatellite instability, has been thought to be closely related to tumor microenvironment and immunotherapy.MethodsIn this study, the 357 HCC samples were download from The Cancer Genome Atlas (TCGA) and analyzed.ResultsSingle nucleotide polymorphism (SNP) and C > T variation had the most missense mutations, and we also observed the higher mutation frequency in TP53, TTN, CTNNB1. With an optimal cut-off value of 4.61, the high level of TMB presented a worse prognosis. Functional analysis of the differentially expressed genes (DEGs) showed they were enriched in the pathway of the formation of extracellular matrix organization and sulfur compound metabolic. A 5-gene-based (including SFRP4, IL7R, FBLN2, COLEC10 and CHGA) model has been constructed to explore the independent prognosis capacity of each HCC patient.ConclusionsThe establishment of 5-gene-based prognosis model functions well in predicting the median of 1- , 3- and 5-year outcome of the individual patient and which will be beneficial for pre-clinical diagnosis and therapeutic decision-making.

Comprehensive assessment of PD-L1 and PD-L2 dysregulation in gastrointestinal cancers

Epigenomics ◽  
2020 ◽  
Author(s):  
Qijie Zhao ◽  
Jinan Guo ◽  
Yueshui Zhao ◽  
Jing Shen ◽  
Parham Jabbarzadeh Kaboli ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Signaling Pathways ◽  
Underlying Mechanism ◽  
Comprehensive Analysis ◽  
The Cancer Genome Atlas ◽  
Gastrointestinal Cancers ◽  
Tumor Mutation Burden ◽  
Mutation Burden ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Background: PD-L1 and PD-L2 are ligands of PD-1. Their overexpression has been reported in different cancers. However, the underlying mechanism of PD-L1 and PD-L2 dysregulation and their related signaling pathways are still unclear in gastrointestinal cancers. Materials & methods: The expression of PD-L1 and PD-L2 were studied in The Cancer Genome Atlas and Genotype-Tissue Expression databases. The gene and protein alteration of PD-L1 and PD-L2 were analyzed in cBioportal. The direct transcription factor regulating PD-L1/ PD-L2 was determined with ChIP-seq data. The association of PD-L1/PD-L2 expression with clinicopathological parameters, survival, immune infiltration and tumor mutation burden were investigated with data from The Cancer Genome Atlas. Potential targets and pathways of PD-L1 and PD-L2 were determined by protein enrichment, WebGestalt and gene ontology. Results: Comprehensive analysis revealed that PD-L1 and PD-L2 were significantly upregulated in most types of gastrointestinal cancers and their expressions were positively correlated. SP1 was a key transcription factor regulating the expression of PD-L1. Conclusion: Higher PD-L1 or PD-L2 expression was significantly associated with poor overall survival, higher tumor mutation burden and more immune and stromal cell populations. Finally, HIF-1, ERBB and mTOR signaling pathways were most significantly affected by PD-L1 and PD-L2 dysregulation. Altogether, this study provided comprehensive analysis of the dysregulation of PD-L1 and PD-L2, its underlying mechanism and downstream pathways, which add to the knowledge of manipulating PD-L1/PD-L2 for cancer immunotherapy.

scholarly journals Exceptional Chemotherapy Response in Metastatic Colorectal Cancer Associated With Hyper-Indel–Hypermutated Cancer Genome and Comutation of POLD1 and MLH1

2017 ◽  
pp. 1-12
Author(s):  
Manish R. Sharma ◽  
James T. Auman ◽  
Nirali M. Patel ◽  
Juneko E. Grilley-Olson ◽  
Xiaobei Zhao ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Colon Cancer ◽  
Somatic Mutation ◽  
Mutation Rate ◽  
Germ Line ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Response To Chemotherapy ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Purpose A 73-year-old woman with metastatic colon cancer experienced a complete response to chemotherapy with dose-intensified irinotecan that has been durable for 5 years. We sequenced her tumor and germ line DNA and looked for similar patterns in publicly available genomic data from patients with colorectal cancer. Patients and Methods Tumor DNA was obtained from a biopsy before therapy, and germ line DNA was obtained from blood. Tumor and germline DNA were sequenced using a commercial panel with approximately 250 genes. Whole-genome amplification and exome sequencing were performed for POLE and POLD1. A POLD1 mutation was confirmed by Sanger sequencing. The somatic mutation and clinical annotation data files from the colon (n = 461) and rectal (n = 171) adenocarcinoma data sets were downloaded from The Cancer Genome Atlas data portal and analyzed for patterns of mutations and clinical outcomes in patients with POLE- and/or POLD1-mutated tumors. Results The pattern of alterations included APC biallelic inactivation and microsatellite instability high (MSI-H) phenotype, with somatic inactivation of MLH1 and hypermutation (estimated mutation rate > 200 per megabase). The extremely high mutation rate led us to investigate additional mechanisms for hypermutation, including loss of function of POLE. POLE was unaltered, but a related gene not typically associated with somatic mutation in colon cancer, POLD1, had a somatic mutation c.2171G>A [p.Gly724Glu]. Additionally, we noted that the high mutation rate was largely composed of dinucleotide deletions. A similar pattern of hypermutation (dinucleotide deletions, POLD1 mutations, MSI-H) was found in tumors from The Cancer Genome Atlas. Conclusion POLD1 mutation with associated MSI-H and hyper-indel–hypermutated cancer genome characterizes a previously unrecognized variant of colon cancer that was found in this patient with an exceptional response to chemotherapy.

scholarly journals Exploring the Pathological Mechanism of Bladder Cancer Based on Tumor Mutational Burden Analysis

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Yao Ma ◽  
Xiao-Fei Feng ◽  
Wan-Xia Yang ◽  
Chong-Ge You
Keyword(s):  
Bladder Cancer ◽  
High Throughput Sequencing ◽  
The Cancer Genome Atlas ◽  
Bladder Neoplasm ◽  
Urinary Bladder Neoplasm ◽  
Related Data ◽  
Mutation Burden ◽  
Tumor Mutational Burden ◽  
Cancer Genome Atlas ◽  
Tumor Genome

Although immunotherapy has progressed in the treatment of bladder cancer, some patients still have poor prognosis. New therapeutic targets are eager to be discovered to improve the outcomes of bladder cancer. With the development of high-throughput sequencing and tumor profiling, potential tumor biomarkers were identified. Through the interpretation of related data from the Cancer Genome Atlas database (TCGA), some key genes have been discovered to drive the development and prognosis of urinary bladder neoplasm. On account of the success of immunotherapy in many cancer types, we established the relationship between tumor mutation burden and immune microenvironment of bladder cancer and found the changes of several immune cells in this disease. Based on the understanding of the bladder tumor genome and immune environment, this study is supposed to provide new therapies for the treatment of bladder neoplasm.

scholarly journals FXR silencing in human colon cancer by DNA methylation and KRAS signaling

2014 ◽  
Vol 306 (1) ◽  
pp. G48-G58 ◽  
Author(s):  
Ann M. Bailey ◽  
Le Zhan ◽  
Dipen Maru ◽  
Imad Shureiqi ◽  
Curtis R. Pickering ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Colon Cancer ◽  
Epithelial To Mesenchymal Transition ◽  
Human Colon ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Human Colon Cancer ◽  
Mesenchymal Transition ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Farnesoid X receptor (FXR) is a bile acid nuclear receptor described through mouse knockout studies as a tumor suppressor for the development of colon adenocarcinomas. This study investigates the regulation of FXR in the development of human colon cancer. We used immunohistochemistry of FXR in normal tissue ( n = 238), polyps ( n = 32), and adenocarcinomas, staged I–IV ( n = 43, 39, 68, and 9), of the colon; RT-quantitative PCR, reverse-phase protein array, and Western blot analysis in 15 colon cancer cell lines; NR1H4 promoter methylation and mRNA expression in colon cancer samples from The Cancer Genome Atlas; DNA methyltransferase inhibition; methyl-DNA immunoprecipitation (MeDIP); bisulfite sequencing; and V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) knockdown assessment to investigate FXR regulation in colon cancer development. Immunohistochemistry and quantitative RT-PCR revealed that expression and function of FXR was reduced in precancerous lesions and silenced in a majority of stage I-IV tumors. FXR expression negatively correlated with phosphatidylinositol-4, 5-bisphosphate 3 kinase signaling and the epithelial-to-mesenchymal transition. The NR1H4 promoter is methylated in ∼12% colon cancer The Cancer Genome Atlas samples, and methylation patterns segregate with tumor subtypes. Inhibition of DNA methylation and KRAS silencing both increased FXR expression. FXR expression is decreased early in human colon cancer progression, and both DNA methylation and KRAS signaling may be contributing factors to FXR silencing. FXR potentially suppresses epithelial-to-mesenchymal transition and other oncogenic signaling cascades, and restoration of FXR activity, by blocking silencing mechanisms or increasing residual FXR activity, represents promising therapeutic options for the treatment of colon cancer.

scholarly journals Spatial heterogeneity and organization of tumor mutation burden and immune infiltrates within tumors based on whole slide images correlated with patient survival in bladder cancer

2019 ◽  
Author(s):  
Hongming Xu ◽  
Sunho Park ◽  
Jean René Clemenceau ◽  
Jinhwan Choi ◽  
Nathan Radakovich ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Spatial Heterogeneity ◽  
Tumor Cells ◽  
Tumor Infiltrating Lymphocytes ◽  
The Cancer Genome Atlas ◽  
Mutation Burden ◽  
Prognostic Utility ◽  
Cancer Genome Atlas ◽  
Infiltrating Lymphocytes ◽  
Whole Slide Images

AbstractHigh-TMB (TMB-H) could result in an increased number of neoepitopes from somatic mutations expressed by a patient’s own tumor cell which can be recognized and targeted by neighboring tumor-infiltrating lymphocytes (TILs). Deeper understanding of spatial heterogeneity and organization of tumor cells and their neighboring immune infiltrates within tumors could provide new insights into tumor progression and treatment response. Here we developed and applied computational approaches using digital whole slide images (WSIs) to investigate spatial heterogeneity and organization of regions harboring TMB-H tumor cells and TILs within tumors, and its prognostic utility. In experiments using WSIs from The Cancer Genome Atlas bladder cancer (BLCA), our findings show that WSI-based approaches can reliably predict patient-level TMB status and delineate spatial TMB heterogeneity and co-organization with TILs. TMB-H patients with low spatial heterogeneity enriched with high TILs show improved overall survival indicating a prognostic role of spatial TMB and TILs information in BLCA.

scholarly journals Cancer Type-Dependent Correlations betweenTP53Mutations and Antitumor Immunity

2019 ◽  
Author(s):  
Lin Li ◽  
Mengyuan Li ◽  
Xiaosheng Wang
Keyword(s):  
Antitumor Immunity ◽  
Colon Adenocarcinoma ◽  
Joint Effect ◽  
The Cancer Genome Atlas ◽  
Cancer Type ◽  
Mutation Burden ◽  
Cancer Genome Atlas ◽  
Negative Role ◽  
Stomach Adenocarcinoma ◽  
Cancer Types

AbstractMany studies have shown thatTP53mutations play a negative role in antitumor immunity. However, a few studies reported thatTP53mutations could promote antitumor immunity. To explain these contradictory findings, we analyzed five cancer cohorts from The Cancer Genome Atlas (TCGA) project. We found thatTP53-mutated cancers had significantly higher levels of antitumor immune signatures thanTP53-wildtype cancers in breast invasive carcinoma (BRCA) and lung adenocarcinoma (LUAD). In contrast,TP53-mutated cancers had significantly lower antitumor immune signature levels thanTP53-wildtype cancers in stomach adenocarcinoma (STAD), colon adenocarcinoma (COAD), and head and neck squamous cell carcinoma (HNSC). Moreover,TP53-mutated cancers likely had higher tumor mutation burden (TMB) and tumor aneuploidy level (TAL) thanTP53-wildtype cancers. However, the TMB differences were more marked betweenTP53-mutated andTP53-wildtype cancers than the TAL differences in BRCA and LUAD, and the TAL differences were more significant in STAD and COAD. Furthermore, we showed that TMB and TAL had a positive and a negative correlation with antitumor immunity and that TMB affected antitumor immunity more greatly than TAL did in BRCA and LUAD while TAL affected antitumor immunity more strongly than TMB in STAD and HNSC. These findings indicate that the distinct correlations betweenTP53mutations and antitumor immunity in different cancer types are a consequence of the joint effect of the altered TMB and TAL caused byTP53mutations on tumor immunity. Our data suggest that theTP53mutation status could be a useful biomarker for cancer immunotherapy response depending on cancer types.

scholarly journals The LIM Protein Ajuba Augments Tumor Metastasis in Colon Cancer

Cancers ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1913
Author(s):  
Noëlle Dommann ◽  
Daniel Sánchez-Taltavull ◽  
Linda Eggs ◽  
Fabienne Birrer ◽  
Tess Brodie ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Cell Lines ◽  
Human Colon ◽  
Tumor Burden ◽  
The Cancer Genome Atlas ◽  
Cancer Tissue ◽  
Potential Candidate ◽  
Sequencing Data ◽  
Human Colon Cancer ◽  
Cancer Genome Atlas

Colorectal cancer, along with its high potential for recurrence and metastasis, is a major health burden. Uncovering proteins and pathways required for tumor cell growth is necessary for the development of novel targeted therapies. Ajuba is a member of the LIM domain family of proteins whose expression is positively associated with numerous cancers. Our data shows that Ajuba is highly expressed in human colon cancer tissue and cell lines. Publicly available data from The Cancer Genome Atlas shows a negative correlation between survival and Ajuba expression in patients with colon cancer. To investigate its function, we transduced SW480 human colon cancer cells, with lentiviral constructs to knockdown or overexpress Ajuba protein. The transcriptome of the modified cell lines was analyzed by RNA sequencing. Among the pathways enriched in the differentially expressed genes, were cell proliferation, migration and differentiation. We confirmed our sequencing data with biological assays; cells depleted of Ajuba were less proliferative, more sensitive to irradiation, migrated less and were less efficient in colony formation. In addition, loss of Ajuba expression decreased the tumor burden in a murine model of colorectal metastasis to the liver. Taken together, our data supports that Ajuba promotes colon cancer growth, migration and metastasis and therefore is a potential candidate for targeted therapy.

scholarly journals CXCL11 Correlates with Anti-tumor Immune Microenvironment and Improved Prognosis in Colon Cancer

2020 ◽  
Author(s):  
Yingying Cao ◽  
Youwei Zhang ◽  
Nanlin Jiao ◽  
Tiantian Sun ◽  
Yanru Ma ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Tumor Development ◽  
Specific Effect ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Immune Microenvironment ◽  
Antibody Treatment ◽  
Tumor Immune Microenvironment ◽  
Cancer Genome Atlas ◽  
Immunological Regulation

Abstract Background: CXCL11 has been considered to be responsible for tumor development, but the specific effect of CXCL11 in colon cancer was still obscure. Therefore, the prognostic value and immunological regulation effect of CXCL11 in colon cancer were evaluated in this study.Methods: Three independent datasets were used for mRNA-related analysis: one dataset from the Cancer Genome Atlas (TCGA, n=451) and two single-cell RNA sequencing (scRNA-seq) datasets from Gene Expression Omnibus (GEO): GSE146771 and GSE132465. In addition, the patient cohort (the Yijishan Hospital cohort, YJSHC, n=108) was utilized for cell infiltration-related analysis, accordingly. Both CXCL11 mRNA expression and CXCL11+ (CXCL11-producing) cells were assessed in colon cancer, whose effect on prognosis and immunological regulation was also studied. Results: High CXCL11 expression were associated with better prognosis in colon cancer, which was still significant even if clinicopathological factors were adjusted. Furthermore, CXCL11 positively correlated with anti-tumor cells infiltration, such as CD8+ T cells and natural killer cells. Meanwhile, CXCL11 correlated positively with several genes associated with DC, NK and T recruitment，and a gene set of cytotoxic genes. Notably, CXCL11 correlated positively with several immune checkpoint related genes including of PD-L1. Conclusions: CXCL11 contributed to anti-tumor immune microenvironment and could improve prognosis in patients with colon cancer. Especially, it’s a potential approach that inducible expression of CXCL11 by genetic and pharmacological interventions is able to improve prognosis and response to anti-PD-1 (programmed cell death protein-1) antibody treatment in colon cancer. However, it requires to be verified by further prospective investigations.

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