Measuring the effects of radiotherapy on DNA methylation in colorectal cancer.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e15089-e15089
Author(s):  
Jedi Maher ◽  
Graeme P Young ◽  
Susanne Kartin Pedersen ◽  
Erin L. Symonds
Keyword(s):  
Colorectal Cancer ◽  
Response To Therapy ◽  
Blood Levels ◽  
Cancer Tissue ◽  
Tissue Samples ◽  
Tumor Tissues ◽  
Low Levels ◽  
Original Size ◽  
Cancer Tissues ◽  
Monitoring Response

e15089 Background: BCAT1 and IKZF1are methylated with high frequency in colorectal cancer (CRC). This study aimed to investigate the level of methylation in these two genes in tissue samples from CRC patients who had undergone radiotherapy. Methods: Tumor and adjacent non-tumor tissue was collected from 50 CRC patients, including 14 subjected to radiotherapy prior to surgical resection. DNA was extracted, bisulfite converted and the levels of methylated BCAT1 and IKZF1 DNA were expressed as the percentage of 5ng tissue DNA (normalized to ACTB levels). Results: In the 36 CRC patients who did not receive radiotherapy prior to resection, tumor tissues had high levels of methylated BCAT1 and IKZF1 compared with adjacent non-tumor tissues (p < 0.001, Table). The CRC tissues from the 14 patients who received radiotherapy pre-surgery had significantly lower levels of methylation compared to the levels in tumors from non-treated patients (p<0.01, Table). Radiotherapy did not appear to affect the methylated BCAT1/IKZF1DNA levels in adjacent non-cancer tissues (p > 0.05, Table). In this limited dataset, a correlation was observed with %methylation and response to radiotherapy measured based on tumor size relative to original size, with the lowest methylation in the tumors associated with the greatest downsizing. Conclusions: The high levels of methylated BCAT1 and IKZF1 in CRC tissue and the low levels in the surrounding non-cancer tissue suggest that the markers are tumor specific with no obvious field effect. In contrast, in the samples obtained from patients treated with radiotherapy prior to resection, the methylation levels in CRC tissues were similar to the levels measured in the adjacent non-tumor tissues. Further studies are necessary to determine the reason for this and whether it has implications for monitoring response to therapy based on blood levels of methylated BCAT1 and IKZF1. [Table: see text]

scholarly journals Cytogenetic differences in blood and cancer tissue samples of the same patient group

2020 ◽  
Vol 4 (1) ◽  
pp. 01-03
Author(s):  
Osman Demirhan ◽  
Deniz Taştemir Korkmaz ◽  
Nesrin Çetinel
Keyword(s):  
Malignant Disease ◽  
Chromosomal Abnormalities ◽  
Cancer Tissue ◽  
Tissue Samples ◽  
Genetic Changes ◽  
Tumor Tissues ◽  
Cancer Tissues ◽  
Gene Expression Alterations ◽  
Breast Tissues ◽  
Improved Methods

Breast cancer (BC) is the most prevalent malignant disease in females worldwide. Genomic instability in tumor tissue has been associated with tumor progression. These genetic changes may take a variety of forms, including numerical and structural chromosomal abnormalities (CAs), epigenetic changes, and gene expression alterations. Many tumor tissues are made up of genetically different cell populations, and the study of the causes and consequences of this heterogeneity play a central role in cancer research. In this study, CAs in blood and cancer tissues of patients with sporadic BC were examined. Our findings shows that the increase in numerical sex aneuploidy in BC tissues is significantly higher than in blood tissue. These aneuploidy increases in cancer tissues seem to be compatible with the development and increase of cancer, and can play a role in the pathogenesis of cancers. These changes are consistent with early and long-standing exposure to carcinogens, especially estrogens. These findings should clarify our understanding of breast carcinogenesis in breast tissues and promote development of improved methods for risk assessment and BC prevention in women.

Genetic diversity of HPV in tissues of tumors of the reproductive organs in women.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e17001-e17001
Author(s):  
Galina Andreevna Nerodo ◽  
Oleg Ivanovich Kit ◽  
Tatiana Zykova ◽  
Victoria A. Ivanova ◽  
Vera P. Nikitina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cervical Cancer ◽  
Vulvar Cancer ◽  
Uterine Cancer ◽  
Reproductive Organs ◽  
Cancer Tissue ◽  
Hpv 16 ◽  
Tissue Samples ◽  
Tumor Tissues ◽  
Cancer Tissues

e17001 Background: The purpose of the study was to determine the rate of various HPV genotypes detection in tissues of tumors of the female reproductive organs. Methods: FFPE and frozen tissue samples of cervical cancer (n=126), vulvar cancer (n=113) and uterine cancer (n=29) were studied. DNAs of HPV 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58 and 59 were determined by the Real-Time PCR. Results: HPV DNAs were found in 94.4% of samples of cervical cancer tissue, 65.5% - uterine cancer tissue and 28.3% - vulvar cancer tissue. HPV 16 and 18 were the most frequent (78.8%). HPV 16 in cervical cancer was detected in 60.9%, vulvar cancer – 59.0% and uterine cancer – 54.5%. On the contrary, HPV 18 was more frequent in uterine cancer (40.9%) and less frequent in cervical cancer (18.4%) and vulvar cancer (2.7%). Besides HPV 16 and 18, genotypes 31, 33, 35, 39, 45, 51, 52, 56 and 59 were found in tumor tissues as well (21.2% in total). HPV 35, 52 and 56 were the most frequently detected. Cervical cancer tissues showed the greatest genetic diversity of HPV and uterine cancer tissues – the lesser one (HPV 35 only, besides HPV 16 and 18). Combination of several HPV types was also more frequent in cervical cancer (37.0% of positive samples); in vulvar cancer – 18.8% and in uterine cancer – 15.8%. Conclusions: The results confirm HPV significance in carcinogenesis of cervical cancer, vulvar cancer and probably uterine cancer and show genetic diversity of HPV in different localizations of tumors of the female reproductive system.

scholarly journals Hypermethylated miR-424 in Colorectal Cancer Subsequently Upregulates VEGF

2021 ◽  
Author(s):  
Zahra Nouri Ghonbalani ◽  
Shiva Shahmohamadnejad ◽  
Parvin Pasalar ◽  
Ehsan Khalili
Keyword(s):  
Colorectal Cancer ◽  
Cancer Cells ◽  
Cancer Progression ◽  
Promoter Region ◽  
Hct116 Cell ◽  
Methylation Status ◽  
Expression Level ◽  
Cancer Tissue ◽  
Vegf Expression ◽  
Cancer Tissues

Abstract PurposeColorectal cancer (CRC) is the second leading cause of death from cancer in adults. Recent advances have shown that cancer cells can have some epigenetic changes involved in all stages of cancer. It has also been shown that miR-424 acts as gene expression regulators in many biological processes, including angiogenesis with mediators such as VEGF. In the current study, to identify the potential role of miR-424 in colorectal cancer progression, methylation status of miR-424 promoter region and its expression level have been evaluated. Besides, the correlation between VEGF level and miR-424 expression level has been assessed.MethodsMethylation status miR-424 promoter was assessed using methylation-specific polymerase chain reaction (MSP). The expression level of miR-424 in human colorectal cancer tissue was analyzed by quantitative PCR. HCT116 cell line was selected to evaluate the correlation between the miR-424 expression level and the promoter's methylation status. VEGF expression, one out of mir-424 targets involved in angiogenesis and cancer progression, was measured by western blot analysis in the pairs of cancer tissues and their adjacent tissues.ResultsOur results have revealed that the promoter region of miR-424 is methylated in cancer cells compared to normal cells, leading to down-regulation of miR-424 in the colorectal cancer tissues compared to the normal tissues. Also, we found that the expression protein's level of VEGF in the tumor cells increased compared with normal tissues.ConclusionThe present study suggests that hypermethylation downregulates miR-424. VEGF expression is upregulated with decreased miR-424 in colorectal cancer, which results in cancer progression.

Blood-based screening for methylation changes in colorectal cancer patients using novel nanotechnologies.

2013 ◽  
Vol 31 (4_suppl) ◽  
pp. 384-384
Author(s):  
Nita Ahuja ◽  
Ruby Kwak ◽  
Brian Keeley ◽  
Alejandro Stark ◽  
Angela Anna Guzzetta ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Screening ◽  
Cancer Patients ◽  
Methylation Status ◽  
High Sensitivity ◽  
Single Copy ◽  
Tissue Samples ◽  
Methylation Frequency ◽  
Colorectal Cancer Patients ◽  
Cancer Tissues

384 Background: Identification of blood-based biomarkers for cancer screening is essential in order to develop novel and minimally invasive methods for colorectal cancer screening. Our lab has successfully applied a novel nanotechnology that allows us to detect and amplify a single tumor DNA fragment in a plasma sample. This DNA is tested for methylation of several genes including TFPI2 which has shown to be highly sensitive and specific for the detection colorectal cancer in stool. Methods: Whole blood was obtained from 18 colorectal cancer patients and plasma was isolated. Plasma was processed using Methylation On Beads nanotechnology (MOB) and bisulfate treated. Methylation status was determined via quantitative PCR method. Results: Two genes, TFPI2 and IGFBP3, were detected with a high sensitivity. TFPI2, demonstrated a methylation frequency of 94.4%, which is concordant with the TFPI2 methylation frequency of 99% in primary colorectal cancer tissues. IGFBP3 showed the methylation frequency of 61.1%, which corresponds with the methylation frequency of 52% in retrospective colorectal cancer tissues in previous studies. Quantification using standard curves indicated a single copy level of DNA found in plasma. Conclusions: Blood-based screening is challenging due to extremely low quantities of circulating DNA in blood. Utilizing a novel nanotechnology that detects DNA at a single copy level, the methylation changes in colorectal cancer were successfully detected in plasmas at similar frequencies as in tissue samples. This study has demonstrated the feasablility and applicability to blood-based screening. Future studies will focus on improving the sensitivity and determining the specificity of this method.

scholarly journals Non-small cell lung cancer microbiota characterization: Prevalence of enteric and potentially pathogenic bacteria in cancer tissues

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249832
Author(s):  
Nathan Dumont-Leblond ◽  
Marc Veillette ◽  
Christine Racine ◽  
Philippe Joubert ◽  
Caroline Duchaine
Keyword(s):  
Lung Cancer ◽  
Pathogenic Bacteria ◽  
Amplicon Sequencing ◽  
Healthy Tissue ◽  
Cancer Tissue ◽  
Rrna Gene ◽  
Variable Degree ◽  
Tissue Samples ◽  
Small Cancer ◽  
Cancer Tissues

Following recent findings linking the human gut microbiota to gastrointestinal cancer and its treatment, the plausible relationship between lung microbiota and pulmonary cancer is explored. This study aims at characterizing the intratumoral and adjacent healthy tissue microbiota by applying a 16S rRNA gene amplicon sequencing protocol to tissue samples of 29 non-small cancer patients. Emphasis was put on contaminant management and a comprehensive comparison of bacterial composition between cancerous and healthy adjacent tissues of lung adenocarcinoma and squamous cell carcinoma is provided. A variable degree of similarity between the two tissues of a same patient was observed. Each patient seems to possess its own bacterial signature. The two types of cancer tissue do not have a distinct bacterial profile that is shared by every patient. In addition, enteric, potentially pathogenic and pro-inflammatory bacteria were more frequently found in cancer than healthy tissue. This work brings insights into the dynamic of bacterial communities in lung cancer and provides prospective data for more targeted studies.

scholarly journals The expression and Clinical Significance of miRNA-135a and Bach1 in colorectal cancer

2021 ◽  
Author(s):  
Yang zhi Jiang ◽  
Qing Guo Tao ◽  
fei yan Zhu
Keyword(s):  
Colorectal Cancer ◽  
Colon Cancer ◽  
Clinical Information ◽  
Control Group ◽  
Tumor Control ◽  
Cancer Tissue ◽  
Expression Levels ◽  
Real Time Quantitative Pcr ◽  
Normal Tissues ◽  
Cancer Tissues

BACKGROUND AIM To explore the correlation between the expression of miRNA-135a and Bach1 in colorectal cancer tissue and the patient's clinical information.  Methods   60 patients with colorectal carcinoma were treated as a control group. Real-time quantitative PCR assays and immunohistochemistry method were performed to detect the expression of miRNA-135a and Bach1 in 60 colorectal carcinomas and adjacent normal tissues, and the clinical and pathological classifications had also been investigated. The SPSS 19.00 software was used. All data represented mean±SD of three independent experiments. P&lt;0.05 was considered statistically significant. Results  miRNA-135a expression levels increased significantly in the colon cancer tissues compared with the non-tumor control tissues(P&lt;0.01). miRNA-135a expression levels were higher in stage III/IV than in stage I/II colon cancer patients. The expression level of Bach1 in colorectal cancer was significantly lower(P&lt;0.01). Bach1 and miRNA-135a were negatively correlated.  Conclusions:  The levels of miRNA-135a and Bach1 were opposite, the over-expression of miRNA-135a might downregulated the expression of Bach1, which might be involved in the pathogenesis of colorectal cancer.

scholarly journals The Impact of Freezing Temperature and Pretreatment Protocol on Solid Phase HR-MAS-MRS Metabolomes of Colorectal Cancer Tissue

2021 ◽  
Author(s):  
Hui Liu ◽  
Yu Wang ◽  
Yue-qiang Han ◽  
Guang-yu Yang ◽  
Lu Wang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Liquid Nitrogen ◽  
Solid Phase ◽  
Phospholipid Metabolism ◽  
The Other ◽  
Cancer Tissue ◽  
Nitrogen Storage ◽  
Tissue Samples ◽  
Colorectal Cancer Tissue ◽  
Choline Phospholipid

Abstract Background: To explore the best pretreatment method of colorectal cancer tissue samples for metabolomics research based on solid-phase nuclear magnetic resonance. Method: Taking mucosal tissues of colorectal cancer and divide it into 5 groups of 0.2cm*0.2cm*0.2cm. Pretreatment was performed as follows: I. Liquid nitrogen storage; II. Transfer to the -80℃ refrigerator after storing in liquid nitrogen for 10 minutes; III. Transfer to the -80℃ refrigerator after storing in liquid nitrogen for 20 minutes; IV. Transfer to the -80℃ refrigerator after storing in liquid nitrogen for 30 minutes; V. -80℃ refrigerator storage. The interval between tumor sample separation to pretreatment is less than 30 minutes. The tissue sample testing process is carried out on Bruker AVII-600 Spectrometer equipped with a high-resolution probe having a 1H/13C magical angle rotation. The tissue samples were put into the NMR which run at a speed of 5000Hz for 10 minutes. NMR signals were collected and analyzed by Fourier transform, partial least squares discrimination analysis (PLS-DA). Corresponding metabolites and metabolic pathways were found in Human Metabolome Database (HMDB) according to the ppms with variable importance of projection (VIP) ＞1. Results: The content of pelargonic acid, stearic acid, D-Ribose, heptadecanoic acid, pyruvic acid, succinate, sarcosine, glycine, creatine, and L-lactate in liquid nitrogen storage group were significantly lower than the other groups (P<0.05), the content of glycerophosphocholine in liquid nitrogen storage group was lower than the other groups (P=0.055). Pyruvic, succinate and L-lactate are participating in glucose metabolism. Glycerophosphocholine, sarcosine, glycine and creatine are participating in choline phospholipid metabolism. This indicated that the glucose and choline phospholipid metabolism levels of the liquid nitrogen group were significantly lower than those of the other 4 groups. Conclusion: Liquid nitrogen storage can slow down the glucose and choline phospholipid metabolism process of colorectal cancer tissue samples in vitro; liquid nitrogen can preserve tissue sample’s metabolic state in the body. It is therefore the better way to store tissue sample than the other methods. clinical trial registry website: http://www.chictr.org.cn/index.aspx. Trial number: ChiCTR1900024640

scholarly journals Performance of a MethyLight assay for methylated SFRP2 DNA detection in colorectal cancer tissue and serum

2019 ◽  
Vol 34 (1) ◽  
pp. 54-59 ◽  
Author(s):  
Hui Li ◽  
Zhenzhen Wang ◽  
Guodong Zhao ◽  
Yong Ma ◽  
Ying Chen ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Screening ◽  
Colorectal Cancer Screening ◽  
Limit Of Detection ◽  
Methylation Status ◽  
Screening Method ◽  
Cancer Tissue ◽  
Non Invasive ◽  
Cancer Tissues ◽  
Methylight Assay

Background: Colorectal cancer is one of the five most common cancers in China, and its incidence is steadily increasing. An accurate and non-invasive screening method is needed to increase the population uptake of colorectal cancer screening. Secreted frizzled-related protein 2 ( SFRP2) has been found to be hypermethylated in most colorectal cancer patients, and it may fulfill the role of a non-invasive biomarker for colorectal cancer screening. Methods: Methylation status of SFRP2 was examined in 17 cancer tissues and paired adjacent paracancer tissues by a new SFRP2 MethyLight assay, which was also used to test the serum of 62 patients with colorectal cancer and 55 normal individuals. Results: The limit of detection of the SFRP2 MethyLight assay was about 200 pg per reaction. The SFRP2 methylation level was higher in 94.1% colorectal cancer tissues than in paired adjacent paracancer tissues ( P<0.001). The sensitivity and specificity of SFRP2 for detecting colorectal cancer in serum were 69.4% (95% confidence interval (CI) 56.2, 80.1%) and 87.3% (95% CI 74.9, 94.3%), respectively. Conclusion: SFRP2 methylation in serum has the potential to be a non-invasive biomarker for colorectal cancer screening.

MYC gene copy number (GCN) and sensitivity to anti-EGFR monoclonal antibodies in metastatic colorectal cancer (mCRC).

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. e21018-e21018
Author(s):  
Armida D'Incecco ◽  
Lorenza Landi ◽  
George Fountzilas ◽  
Konstantine T. Kalogeras ◽  
Ravit Geva ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Monoclonal Antibodies ◽  
Rare Event ◽  
Gene Copy Number ◽  
Growth Factor Receptor ◽  
Progression Free Survival ◽  
Gene Copy ◽  
Cancer Tissue ◽  
Tissue Samples ◽  
Myc Gene

e21018 Background: Monoclonal antibodies against Epidermal Growth Factor Receptor (EGFR) demonstrated efficacy in mCRC patients without mutations in the KRAS gene. Previous data in breast and lung cancer suggested that MYC GCN affects sensitivity to anti-EGFR agents. Methods: This retrospective study was conducted in a cohort of 303 mCRC patients treated with cetuximab/panitumumab, either alone (N=24) or in combination with chemotherapy (N=279). MYC GCN was assessed by fluorescence in situ hybridization (FISH) in primary colorectal cancer tissue samples. Results: In the study population response rate (RR) was 28%, median progression-free survival (PFS) 5.6 months and median overall survival (OS) 11.8 months. MYC was successfully evaluated in 298 cases and was amplified in 17 patients (5.7%). Individuals with MYC amplification showed a trend for a lower RR (7.7% versus 28.9%, p=0.12), shorter PFS (3.0 months versus 5.8 months, p=0.22) and shorter OS (11.3 months versus 12.6 months, p=0.15) than patients with non-amplified tumors. A Receiver Operating Characteristic (ROC) analysis was also performed in order to verify whether a better MYC GCN cut-off could discriminate between anti-EGFR sensitive and resistant cases. In this analysis, patients with mean MYC GCN ≥2.53 (N=199, 66.8%) had a significantly higher RR (32.2% versus 19.1%, p=0.02), a longer PFS (5.8 months versus 4.5 months, p=0.06) and a longer OS (12.3 months versus 11.4 months, p=0.59) than patients with mean GCN <2.53 (N=99, 33.2%). In order to assess the potential confounding effect of KRAS and BRAF status, we further analyzed the outcome of the 81 KRAS/BRAF wild-type patients according to MYC GCN. In this subset, a trend for improved RR (42% versus 20%, p=0.05), PFS (8.6 months versus 4.2 months, p=0.16) and OS (13.5 months versus 9.7 months, p=0.51) favored MYC FISH GCN ≥2.73 patients. Conclusions: MYC amplification is a rare event in mCRC, not significantly reducing sensitivity to anti-EGFR agents. A trend for better outcome was observed in presence of increased MYC GCN.

Specificity of methylated BCAT1 and IKZF1 for colorectal cancer.

2018 ◽  
Vol 36 (4_suppl) ◽  
pp. 580-580
Author(s):  
Erin L. Symonds ◽  
Beibei Yao ◽  
Susanne Kartin Pedersen ◽  
David Murray ◽  
Graeme P Young
Keyword(s):  
Colorectal Cancer ◽  
Oesophageal Cancer ◽  
Circulating Tumor Dna ◽  
Cancer Tissue ◽  
Neoplastic Tissue ◽  
Invasive Adenocarcinoma ◽  
Screening And Surveillance ◽  
Adenocarcinoma Of The Prostate ◽  
Cancer Tissues ◽  
Tumor Dna

580 Background: Methylated BCAT1 and IKZF1 are useful circulating tumor DNA (ctDNA) biomarkers for detection and following the course of colorectal cancer (CRC). This study aimed to determine the specificity of methylated BCAT1/ IKZF1 for CRC detection by assaying specimens from patients with other adenocarcinomas. Methods: Blood was collected from patients with invasive adenocarcinoma of the prostate (n = 32), breast (16), oesophagus (15) or colon/rectum (212), prior to any treatment or resection, and from 245 clinically assessed controls with no known prior or current adenocarcinoma. Biopsies were collected from cancer tissue and adjacent non-neoplastic tissue either prior to treatment or at surgery from 9 prostate, 26 breast, 6 oesophagus, 15 CRC cases. All specimens were assayed for methylated BCAT1 and IKZF1 DNA. Calculation of positivity rates: tissue, the proportion of tissue cases with ≥ 5% methylation; blood, the proportion of cases with any detectable signal of either marker. Results: ctDNA positivity rates were significantly higher in CRC (126/212, 59.4%, 95% CI: 52.5 - 66.1) and oesophageal cancer (6/16, 33.3%, 11.0 - 58.7) cases only compared to controls (16/245, 6.5%, 3.8 - 10.4; p < 0.01). ctDNA was more likely to be positive in late stage cancers, although only significant for CRC, Table. Cancer tissue positivity rates were: CRC, 15/15, 100% (96.4 - 100); oesophageal, 5/6, 83.3% (35.9 - 99.6); prostate, 4/9, 44.4% (13.7 - 78.8); breast, 5/26, 19.2% (6.6 - 39.4). All cancer tissues had significantly higher methylation levels than the adjacent tissue (Chi2 test, p >0.05). Conclusions: Only colorectal and oesophageal cancer patients had significantly higher ctDNA positivity rates (using methylated BCAT1/IKZF1) compared to controls. This was also reflected in a higher proportion of cases showing methylation in the cancer tissue. The methylated BCAT1/IKZF1 blood test should be investigated further as a screening and surveillance tool for oesophageal cancer. [Table: see text]

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