genome-wide-analysis-of-dna-methylation-in-gastrointestinal-cancer

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

DNA methylation is an important epigenetic change that is biologically meaningful and a frequent focus of cancer research. Genome-wide DNA methylation is ...

Juntendo University Shizuoka Hospital

A 77-year-old man presented with repeated episodes of melena. He had a medical history of hypertension, atrial fibrillation and cardiogenic brain infarction and took medications, i.e. an antiplatelet agent. Laboratory data revealed iron deficiency anemia. Colonoscopy revealed a yellowish smooth submucosal tumor, 50 mm in diameter, on the Bauhin valve. The lesion was soft and compressible. The overlying mucosa was erosive. CT scan showed a uniform mass with very low density in the ascending colon, corresponding to the above-detected lesion. The clinical diagnosis of colonic lipoma was established. Using a 25 mm electrocautery snare (Olympus, Tokyo, Japan), we transected the upper portion of the mass to unroof the lesion. The mucosa layer was thick and hard. Fat tissue was observed extruding from the cut surface, consistent with the diagnostic hypothesis. After dissecting the overlying mucosa on the anal side by means of an IT knife (Olympus) in order to completely extrude the mass, the fat tissue was further exposed. It took about 26 min to perform the whole procedure. There were no procedure-related complications. Macroscopically, the resected lesion was a yellow solid tumor, 1.6 × 1.5 × 0.7 cm in diameter. Histopathologic examination of the excised specimen confirmed the diagnosis of a lipoma. The clinical course was uneventful. A follow-up endoscopy 1 month later showed a scarred mucosa at the resection site. Similarly, a follow-up CT scan 2 months later revealed no evidence of residual lipoma. The unroofing technique is safe, easy and suitable for the treatment of large lipomas.

Unroofing technique for endoscopic resection of a large colonic lipoma.

Direct hemoperfusion with polymyxin B-immobilized fiber (PMX-DHP) has been reported to improve the outcomes in patients with colorectal perforation. We retrospectively identified prognostic factors in patients with colorectal perforation and considered the efficacy of PMX-DHP based on these prognostic factors.

Analysis of the efficacy of direct hemoperfusion with polymyxin B-immobilized fiber (PMX-DHP) according to the prognostic factors in patients with colorectal perforation.

Gastric cancer with metastases to the scaphoid: a case report.

Prognostic biomarkers are required for risk stratification therapy in the patients with gastrointestinal stromal tumor (GIST). In this study, we aimed to identify prognostic biomarkers in GIST. We assessed the prognostic value of E twenty-six variant 1 (ETV1), a recently identified transcription factor unique to GIST. We also examined the clinical utility and functions of its downstream gene, potassium channel tetramerization domain containing protein 10 (KCTD10).

Gene expression network analysis of ETV1 reveals KCTD10 as a novel prognostic biomarker in gastrointestinal stromal tumor.

The beneficial effects of heparin in the treatment of severe sepsis, septic shock, and sepsis-associated disseminated intravascular coagulation (DIC) have recently been reported. However, the mechanisms underlying the therapeutic benefits of heparin in these conditions have not yet been clearly elucidated. The purpose of this study was to confirm the effect of heparin of neutralizing histone toxicity.

Heparins attenuated histone-mediated cytotoxicity in vitro and improved the survival in a rat model of histone-induced organ dysfunction.

Injury and loss of the endothelial glycocalyx occur during the early phase of sepsis. We previously showed that antithrombin has a protective effect on this structure in vitro. Here, we investigated the possible protective effects of antithrombin in an animal model of sepsis.

Protection of the endothelial glycocalyx by antithrombin in an endotoxin-induced rat model of sepsis.

Esophageal squamous cell carcinoma (ESCC) is common in East Asia and also is often deadly. We sought to determine whether measuring the discoidin domain receptor-1 (DDR1)-both total and phosphorylated proteins-could improve our ability to predict recurrence in ESCC.

Prognostic Impact of Phosphorylated Discoidin Domain Receptor-1 in Esophageal Cancer.

Although primary (PGC) and remnant gastric cancers (RGC) both originate from the same gastrointestinal organ, they have very distinct clinicopathological behaviors. We hypothesized that there would be distinct differences in DNA methylation patterns that would occur during carcinogenesis of RGC and PGC, and that the differences in methylation patterns may help identify the primary factor contributing to chronic inflammation in patients with RGC.

DNA methylation genome-wide analysis in remnant and primary gastric cancers.

Predicting malignancy is important for adequate adjuvant therapy in patients with cancer. Due to cancer being a genetic disease, the detection of gene mutations could be helpful in predicting the prognosis and efficacy of drugs. Gastric cancer is the fifth most common cancer and is the third leading cause of cancer associated mortality worldwide. Mutations in genes may correlate with clinical information in patients with gastric cancer after surgery and, therefore, may be useful for predicting the prognosis of this disease. In the present study, to assess the usefulness of a commercial sequencing panel, TruSeq Amplicon-Cancer Panel (Illumina), using a next-generation sequencer (Illumina MiSeq), mutation analysis of fresh as well as formalin-fixed paraffin-embedded (FFPE) gastric cancer tissues was performed retrospectively. The study group comprised of 4 patients who underwent gastrectomy for gastric cancer. Cancer and normal stomach tissues were collected immediately following surgical removal. Thereafter, the specimens were fixed in 10% neutral formalin for 24-72 h. Normal and FFPE cancer tissues were histologically examined and confirmed. A total of 3 mutations were identified in the driver genes ( and ) in cancer tissues from 2 of the 4 patients, using fresh samples. In addition, FFPE samples were analysed for the same tissues and the same results were obtained by setting the threshold for the percentage of the mutation rate to avoid detection of pseudo-positive mutations. In conclusion, the sequencing analysis using FFPE-derived DNA samples was successfully performed.

Detection of gene mutations in gastric cancer tissues using a commercial sequencing panel.

No difference in the gene methylation status of tumor-suppression genes between pancreatic cancer tissues and adjacent non-cancer tissues is observed. The present study investigated whether the promoter CpG islands of the cysteine dioxygenase 1 (), tachykinin precursor 1 () and checkpoint with forkhead and ring finger domains () genes were methylated in pancreatic cancer and adjacent non-cancerous pancreatic tissue in order to determine if they could be considered as markers for the detection of pancreatic cancer. A total of 38 Formalin-fixed and paraffin-embedded pancreatic adenocarcinoma tissues and their adjacent non-cancerous specimens from patients with pancreatic cancer, as well as 9 non-cancerous pancreatic samples from patients without pancreatic adenocarcinoma were obtained following surgical resection. The hypermethylation of CpG islands was detected using a methylation-specific quantitative PCR. The methylation values were calculated using the ∆Cq method and were expressed as 2. The 2 value of the  promoter from pancreatic adenocarcinoma specimens was significantly higher compared with that of adjacent non-cancerous and tumor-free pancreatic tissues (P<0.0001 and P=0.0008, respectively). The 2 value of the  promoter of pancreatic adenocarcinoma was also significantly higher compared with that of adjacent non-cancerous tissues and tumor-free pancreatic samples (both P<0.0001). However, there was no significant difference in the 2 value of the  promoter among the pancreatic cancer, adjacent non-cancer tissue and tumor-free pancreatic samples. Furthermore, 12 out of the 38 pancreatic adenocarcinoma cases (31.6%) presented some methylation in the  promoter. The results from Kaplan-Meier analysis between  promoter methylation values and the clinicopathological characteristics of patients with pancreatic adenocarcinoma demonstrated that  promoter methylation was significantly associated with lymph node metastasis. The methylation values of  and  promoters in cancer tissues were higher compared with adjacent tissues. However, whether hypermethylation of  and  promoters may serve as a biomarker in the diagnosis of pancreatic adenocarcinoma remains unclear.

Analysis of the methylation of CpG islands in the  and  genes in pancreatic ductal cancer.

Children born to women who experience stress during pregnancy have an increased risk of cancer in later life, but no previous animal studies have tested such a link. We questioned whether prenatal stress in A/J mice affected the development of lung tumors after postnatal response to tobacco specific nitrosamine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Timed-bred A/J mice were randomly assigned on gestation day 12.5 to prenatal stress (PS) by restraint for 5 consecutive days or control (no restraint). Adult offspring of control and stressed pregnancies were all treated with three NNK injections (50 mg/kg every other day) and euthanized 16 weeks later to examine their lungs. Compared to controls, PS dams exhibited significantly increased levels of plasma corticosterone, increased adrenal weights, and decreased fetus weights without fetal loss. Prenatally stressed litters had a significantly higher neonatal death rate within first week of life, and surviving male and female offspring developed lung epithelial proliferations with increase multiplicity, increased area, and aggressive morphology. Prenatal stress also induced more advanced atypical adenomatous hyperplasia (AAH) lesions. We found no difference in lung NNK-derived methyl DNA adducts, but prenatal stress did significantly enhance CD3+ T cell and Foxp3+ T cell tumor infiltration. Prenatal stress significantly increases multiplicity, area of NNK-induced lung tumors and advanced morphology. Prenatal stress did not affect production of NNK-derived methyl DNA adducts but did increase lymphocytic infiltration of lung tumors. To our knowledge, this is the first animal model of prenatal stress with evaluation of cancer development in offspring.

Article	Year
Unroofing technique for endoscopic resection of a large colonic lipoma. Case reports in gastroenterology\| PubMed ID: 22949897	2012
Analysis of the efficacy of direct hemoperfusion with polymyxin B-immobilized fiber (PMX-DHP) according to the prognostic factors in patients with colorectal perforation. Surgery today\| PubMed ID: 23129028	2013
Gastric cancer with metastases to the scaphoid: a case report. Journal of orthopaedic science : official journal of the Japanese Orthopaedic Association\| PubMed ID: 23892427	2015
Gene expression network analysis of ETV1 reveals KCTD10 as a novel prognostic biomarker in gastrointestinal stromal tumor. PloS one\| PubMed ID: 23977394	2013
Heparins attenuated histone-mediated cytotoxicity in vitro and improved the survival in a rat model of histone-induced organ dysfunction. Intensive care medicine experimental\| PubMed ID: 26715580	2015
Protection of the endothelial glycocalyx by antithrombin in an endotoxin-induced rat model of sepsis. Thrombosis research\| PubMed ID: 30216821	2018
Prognostic Impact of Phosphorylated Discoidin Domain Receptor-1 in Esophageal Cancer. The Journal of surgical research\| PubMed ID: 30691832	2019
DNA methylation genome-wide analysis in remnant and primary gastric cancers. Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association\| PubMed ID: 30863929	2019
Detection of gene mutations in gastric cancer tissues using a commercial sequencing panel. Molecular and clinical oncology\| PubMed ID: 31620276	2019
Analysis of the methylation of CpG islands in the and genes in pancreatic ductal cancer. Oncology letters\| PubMed ID: 32194717	2020
Prenatal stress enhances NNK-induced lung tumors in A/J mice. Carcinogenesis\| PubMed ID: 32249286	2020

Koichi Sato

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