scholarly journals Framing the potential of public frameshift peptides as immunotherapy targets in colon cancer

2020 ◽  
Author(s):  
Ide T. Spaanderman ◽  
Fleur S. Peters ◽  
Aldo Jongejan ◽  
Egbert J.W. Redeker ◽  
Cees J.A. Punt ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Cancer Patients ◽  
Mrna Level ◽  
The Cancer Genome Atlas ◽  
Nonsense Mediated Decay ◽  
Reading Frame ◽  
Colon Cancers ◽  
Cancer Genome Atlas ◽  
Frameshift Peptides ◽  
Rna And Dna

AbstractApproximately 15% of Colon Cancers are Microsatellite Instable (MSI). Frameshift Peptides (FPs) formed in MSI Colon Cancer are potential targets for immunotherapeutic strategies. Here we comprehensively characterize the mutational landscape of 71 MSI Colon Cancer patients from the cancer genome atlas (TCGA-COAD). We confirm that the mutations in MSI Colon Cancers are frequently frameshift deletions (23% in MSI; 1% in microsatellite stable), We find that these mutations cluster at specific locations in the genome which are mutated in up to 41% of the patients. We filter these for an adequate variant allele frequency, a sufficient mean mRNA level and the formation of a Super Neo Open Reading Frame (SNORF). Finally, we check the influence of Nonsense Mediated Decay by comparing RNA and DNA sequencing results. Thereby we identify a set of 20 NMD-escaping Public FPs (PFPs) that cover over 90% of MSI Colon Cancer patients and 3 out of 4 Lynch patients in the TCGA-COAD. This underlines the potential for PFP directed immunotherapy, both in a therapeutic and a prophylactic setting.

scholarly journals Framing the potential of public frameshift peptides as immunotherapy targets in colon cancer

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0251630
Author(s):  
Ide T. Spaanderman ◽  
Fleur S. Peters ◽  
Aldo Jongejan ◽  
Egbert J. W. Redeker ◽  
Cornelis J. A. Punt ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Cancer Patients ◽  
Mrna Level ◽  
The Cancer Genome Atlas ◽  
Nonsense Mediated Decay ◽  
Reading Frame ◽  
Colon Cancers ◽  
Cancer Genome Atlas ◽  
Frameshift Peptides ◽  
Rna And Dna

Approximately 15% of Colon Cancers are Microsatellite Instable (MSI). Frameshift Peptides (FPs) formed in MSI Colon Cancer are potential targets for immunotherapeutic strategies. Here we comprehensively characterize the mutational landscape of 71 MSI Colon Cancer patients from the cancer genome atlas (TCGA). We confirm that the mutations in MSI Colon Cancers are frequently frameshift deletions (23% in MSI; 1% in microsatellite stable), We find that these mutations cluster at specific locations in the genome which are mutated in up to 41% of the patients. We filter these for an adequate variant allele frequency, a sufficient mean mRNA level and the formation of a Super Neo Open Reading Frame (SNORF). Finally, we check the influence of Nonsense Mediated Decay (MMD) by comparing RNA and DNA sequencing results. Thereby we identify a set of 20 NMD-escaping Public FPs (PFPs) that cover over 90% of MSI Colon, 62.2% of MSI Endometrial and 58.8% of MSI Stomach cancer patients and 3 out of 4 Lynch patients in the TCGA-COAD. This underlines the potential for PFP directed immunotherapy, both in a therapeutic and a prophylactic setting in multiple types of MSI cancers.

scholarly journals Higher ETV5 Expression Associates With Poor 5-Florouracil-Based Adjuvant Therapy Response in Colon Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Anil K. Giri
Keyword(s):  
Colon Cancer ◽  
Cancer Patients ◽  
Locally Advanced ◽  
Therapy Response ◽  
Predictive Biomarker ◽  
The Cancer Genome Atlas ◽  
Stage Ii ◽  
Epigenetic Mechanism ◽  
Cancer Tissue ◽  
Colon Cancers

Discovery of markers predictive for 5-Fluorouracil (5-FU)-based adjuvant chemotherapy (adjCTX) response in patients with locally advanced stage II and III colon cancer (CC) is necessary for precise identification of potential therapy responders. PEA3 subfamily of ETS transcription factors (ETV1, ETV4, and ETV5) are upregulated in multiple cancers including colon cancers. However, the underlying epigenetic mechanism regulating their overexpression as well as their role in predicting therapy response in colon cancer are largely unexplored. In this study, using gene expression and methylation data from The Cancer Genome Atlas (TCGA) project, we showed that promoter DNA methylation negatively correlates with ETV4 expression (ρ = −0.17, p = 5.6 × 10–3) and positively correlates with ETV5 expression (ρ = 0.22, p = 1.43 × 10–4) in colon cancer tissue. Further, our analysis in 1,482 colon cancer patients from five different cohorts revealed that higher ETV5 expression associates with shorter relapse-free survival (RFS) of adjCTX treated colon cancer patients (Hazard ratio = 2.09–5.43, p = 0.004–0.01). The present study suggests ETV5 expression as a strong predictive biomarker for 5-FU-based adjCTX response in stage II/III CC patients.

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 Alteration in the immune microenvironment based on APC status in MSS/pMMR colon cancer data retrieved from TCGA

2020 ◽  
Author(s):  
Haishan Lin ◽  
Hongchao Zhen ◽  
Kun Shan ◽  
Xiaoting Ma ◽  
Bangwei Cao
Keyword(s):  
Colon Cancer ◽  
Cancer Patients ◽  
Enrichment Analysis ◽  
Tumor Immunotherapy ◽  
Immune Checkpoints ◽  
Immune Microenvironment ◽  
Cancer Data ◽  
T Cell Infiltration ◽  
Colon Cancers ◽  
Tumor Immune Microenvironment

Abstract Immunotherapy is currently the most advanced anti-tumor treatment approach. The efficacy of anti-tumor immunotherapy is closely related to the tumor immune microenvironment, including immune cells, infiltration of immune factors, and expression of immune checkpoints. At present, the biomarkers for predicting the efficacy of colon cancer immunotherapy do not cover all colon cancer patients suitable for immunotherapy. In this study, TCGA database was used to identify tumor genotypes suitable for anti-tumor immunotherapy. We found that some of the MSS/pMMR populations, that were initially considered unsuitable for immunotherapy, might actually be suitable. In APC-wt/MSS colon cancer, the expression of PD-1, PD-L1, CTLA4 and CYT（GZMA and PRF1）were increased. Based on calculations done by ESTIMATE and CIBERSORT algorithms, the ImmunoScore and the proportion of CT8+ T cell infiltration is increased in these patients. Enrichment analysis was done to screen signaling pathways involved in immune response, extracellular matrix, and cell adhesion. Tumors from 42 colon cancer patients, including 22 APC-mt/MSS and 20 APC-wt/MSS, were immunohistochemically evaluated for expression of CD8 and PD-L1. And APC-wt/MSS tumors showed significantly higher expression of CD8 and PD-L1 than APC-mt/MSS tumor. Based on the results, we found that some colon cancers of APC-wt/MSS are classified by Tumor Immune Microenvironment types (TIMTs) TMIT I. So that we speculate that APC-wt/MSS colon cancer patients could benefit from anti-tumor immunotherapy.

scholarly journals Japanese version of The Cancer Genome Atlas, JCGA, established using fresh frozen tumors obtained from 5143 cancer patients

2020 ◽  
Vol 111 (2) ◽  
pp. 687-699 ◽  
Author(s):  
Takeshi Nagashima ◽  
Ken Yamaguchi ◽  
Kenichi Urakami ◽  
Yuji Shimoda ◽  
Sumiko Ohnami ◽  
...  
Keyword(s):  
Cancer Patients ◽  
Japanese Version ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Fresh Frozen ◽  
Cancer Genome Atlas ◽  
Genome Atlas

scholarly journals ExonSkipDB: functional annotation of exon skipping event in human

2019 ◽  
Author(s):  
Pora Kim ◽  
Mengyuan Yang ◽  
Ke Yiya ◽  
Weiling Zhao ◽  
Xiaobo Zhou
Keyword(s):  
Functional Annotation ◽  
Exon Skipping ◽  
Tissue Expression ◽  
The Cancer Genome Atlas ◽  
Multiple Cancer ◽  
Annotation Database ◽  
Reading Frame ◽  
Normal Tissues ◽  
Cancer Genome Atlas ◽  
Functional Features

AbstractExon skipping (ES) is reported to be the most common alternative splicing event due to loss of functional domains/sites or shifting of the open reading frame (ORF), leading to a variety of human diseases and considered therapeutic targets. To date, systematic and intensive annotations of ES events based on the skipped exon units in cancer and normal tissues are not available. Here, we built ExonSkipDB, the ES annotation database available at https://ccsm.uth.edu/ExonSkipDB/, aiming to provide a resource and reference for functional annotation of ES events in multiple cancer and tissues to identify therapeutically targetable genes in individual exon units. We collected 14 272 genes that have 90 616 and 89 845 ES events across 33 cancer types and 31 normal tissues from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx). For the ES events, we performed multiple functional annotations. These include ORF assignment of exon skipped transcript, studies of lost protein functional features due to ES events, and studies of exon skipping events associated with mutations and methylations based on multi-omics evidence. ExonSkipDB will be a unique resource for cancer and drug research communities to identify therapeutically targetable exon skipping events.

scholarly journals The Prognostic Value of the Expression of SMC4 mRNA in Breast Cancer

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Rui-min Ma ◽  
Fan Yang ◽  
Du-ping Huang ◽  
Min Zheng ◽  
Yi-luan Wang
Keyword(s):  
Breast Cancer ◽  
Mrna Expression ◽  
Mrna Level ◽  
The Cancer Genome Atlas ◽  
Paired Samples ◽  
Cancer Genome Atlas ◽  
Advanced Stages ◽  
Independent Risk Factors ◽  
Cancer Tissues ◽  
Structural Maintenance Of Chromosomes

Aim. To investigate the mRNA expression and clinical significance of structural maintenance of chromosomes protein 4 (SMC4) in breast cancer. Methods. A total of 23 paired samples were sequenced, and data from the Cancer Genome Atlas were analyzed. Results. SMC4 mRNA level was significantly upregulated in breast cancer tissues (P<0.001). Patients with high mRNA expression of SMC4 had significantly poor survival (P=0.012). Subgroup analyses show that in nontriple negative breast cancer (non-TNBC) patients, the high SMC4 mRNA expression, older age (>65), negative progesterone receptor, and advanced stages (III-IV) were independent risk factors (HR=3.293, 95% CI 1.257-8.625, P=0.015). In patients with TNBC, high mRNA expression of SMC4 correlated with better survival rate (P<0.046). Conclusion. SMC4 mRNA level is a good prognostic biomarker for patients with breast cancer.

QIM19-124: Does Virtual Navigation Improve Care Continuity and Compliance in Patients With Early Stage Colon Cancer?

2019 ◽  
Vol 17 (3.5) ◽  
pp. QIM19-124
Author(s):  
Dayna Crawford ◽  
Brook Blackmore ◽  
Jeremy Ortega ◽  
Erica Williams
Keyword(s):  
Colon Cancer ◽  
Cancer Patients ◽  
Early Stage ◽  
Stage I ◽  
Stage Iii ◽  
Nccn Guidelines ◽  
Care Continuity ◽  
Colon Cancers ◽  
Follow Up Care

Background: Colon cancer is the 3rd most common cancer in men and women combined, with an occurrence rate of 4.49% for men and 4.15% for women. The 2018 expectation is 50,630 deaths related to colon cancer in the United States (American Cancer Society Facts and Figures 2018). Early detection is increasing with nearly 45% of colon cancers diagnosed as stage I/II (Sarah Cannon Cancer Registry 2015). Treatment for early stage I/II colon cancer patients usually involves surgery then surveillance. On-site navigators perform their duties by patient need and barriers to care. Late stage III/IV colon cancer patients require more assistance and face more barriers, which often leaves early stage I/II patients without an advocate. This disparity can lead to lower rates of follow-up care for early stage I/II patients. Sarah Cannon created a program for virtual colon navigation (VCN) to determine if early stage I/II patients benefit from a virtual navigator who offers support by phone throughout their disease process. Objectives: The goal was to increase early stage I/II patients’ knowledge of their cancer and convey the importance of compliance with follow-up care, such as repeat colonoscopy as recommended by their physician and NCCN Guidelines. Methods: By developing software that utilizes artificial intelligence, Sarah Cannon created an automated process to identify colon cancer patients at the time of diagnosis. This technology then routes positive pathology reports to a VCN who contacts the early stage I/II patients by telephone, ensuring patient connection to the suitable physician for treatment. The VCN helps patients understand their diagnosis, provides education, assesses barriers to care, connects to resources, provides emotional support, and offers assistance with follow-up for physician visits, imaging and procedures such as colonoscopies, based upon NCCN Guidelines and physician guidelines. The VCN also connects stage III/IV patients with an on-site navigator in their region for more hands-on navigation. Results: Through September 2018, Sarah Cannon navigated 734 colon cancers, 332 stage I/II and 402 stage III/IV. With our increased capacity, Sarah Cannon/HCA maintained a 98% rate of follow-up care with new diagnoses of all stages of colon cancer. Conclusions: The VCN program allowed Sarah Cannon/HCA to improve care continuity and compliance based upon NCCN Guidelines for early stage I/II colon cancer patients throughout 5 regions and 37 facilities.

Impact of a simple intervention that improves colon cancer lymph node yield and assessement

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e15058-e15058
Author(s):  
L. Kowalczyk ◽  
P. Shah ◽  
T. George ◽  
L. Lu ◽  
G. Sarosi ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Lymph Node ◽  
Cancer Patients ◽  
Medical Center ◽  
Chi Square ◽  
Lymph Node Yield ◽  
Quality Metric ◽  
Colon Cancers ◽  
National Quality ◽  
Post Test

e15058 Background: The National Quality Forum has endorsed the 12 lymph node (LN) benchmark as a quality metric. Currently, less than 40% of institutions meet this requirement. The purpose of this study was to determine whether implementation of a simple pathology template with dedicated fields for LN reporting led to an increase in the number of colon cancer resections where >12 LNs were reported. Methods: A simple pathology template, derived from the College of American Pathology, using standardized terminology and dedicated fields for LN reporting was implemented in August 2007. Using a pre and post- test design, all consecutive pathology cases were retrospectively reviewed. Inclusion criteria consisted of all stage 0-IV colon cancer patients who underwent surgical resection at a single Veterans Affairs Medical Center. The primary outcome was the percentage of cases in which >12 LNs were assessed between the pre and post-template group. Age, gender, anatomic location, and stage were also collected. Statistical comparisons were made using chi-square and Fisher's exact t-test. Results: 111 pre-template and 71 post-template cases were analyzed. The majority of patients were Caucasian (74%) males (97%). There were no significant differences between the two groups (see Table 1 ), however there was a trend towards more right-sided colon cancers in the pre-template group. 51% of all pre-template pathology reports evaluated >12 LNs compared to 68% of post-template reports (33% improvement in LN yield; p=0.03). Conclusions: Examination of >12 LNs has important therapeutic and prognostic implications in colon cancer patients. Use of a standardized pathology template with dedicated fields for LN reporting is a simple intervention that can increase yield of LN reporting. This can have a significant impact for institutions striving to reach the 12 LN quality metric. [Table: see text] No significant financial relationships to disclose.

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.

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