Promoter methylation data from genomic DNA in patient with rectal cancer
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE39958 | GEO | 2014/08/01
SECONDARY ACCESSION(S): PRJNA172166
REPOSITORIES: GEO
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Project description:The identification of surrogate methylation markers that can predict responses to preoperative chemoradiotherapy (CRT) in rectal cancer patients. Genome-wide association studies in clinical populations are theoretically capable of identifying markers that are capable of tumor regression after CRT. We used InfiniumM-BM-. Methylation Assay to detail methylation status of patientM-bM-^@M-^Ys group showing differential responsiveness to preoperative CRT and profiled SNP biomarkers. The chemoradiosensitivity of tumor tissue from the initial cohort of 45 patients was assessed using clinical responses of tumor regression grade (TRG). TRG was clinically categorized as complete response (CR) as TRG 1, dominant response (ER or finally as DR) as TRG 1 and 2, and efficient response (RYN or finally as ER) as TRG 1, 2, and 3 (TRG grade from Mandard et al, 1994). Examination of genome-wide DNA methylation in 45 colon cancer tissues. We separated patients into TRG1,2,3,4 and 5 group after chemoradiotherapy(CRT). As proposed by Mandard et al. TRG 1, complete tumor response; TRG2, residual cancer cells scattered through fibrosis; TRG 3, an increased number of residual cancer cells, with predominant fibrosis; TRG 4, residual cancer outgrowing fibrosis; and TRG 5, no regressive changes within the tumor: Responders (TRG 1 and 2) and nonresponders (TRG 3?5). Mandard et al. Cancer 1994 Group 1 and Group 2 in ER, CR and RYN was divided by TRG classification. CR: group 1 - TRG 2,3,4 and 5; group 2 - TRG 1 ER: group 1 - TRG 3,4,5; group 2 - TRG 1 and 2 RYN: group 1 - TRG 4 and 5; group 2 - TRG 1,2 and 3
2014-08-01 | E-GEOD-39958 | biostudies-arrayexpress
Project description:The identification of surrogate single nucleotide polymorphism (SNP) markers that can predict responses to preoperative chemoradiotherapy (CRT) in rectal cancer patients. Genome-wide association studies in clinical populations are theoretically capable of identifying markers that are capable of tumor regression after CRT. We used Affymetrix’s SNP Array 6.0 to detail genetic polymorphism of patient’s group showing differential responsiveness to preoperative CRT and profiled SNP biomarkers. The chemoradiosensitivity of tumor tissue from the initial cohort of 43 patients was assessed using clinical responses of tumor regression grade (TRG). TRG was clinically categorized as complete response (CR) as TRG 1, dominant response (ER or finally as DR) as TRG 1 and 2, and efficient response (RYN or finally as ER) as TRG 1, 2, and 3 (TRG grade from Mandard et al, 1994). Blood DNAs were prepared from each patients and hybridized to Affymetrix’s SNP Array 6.0. Genotypes were determined using the Affymetrix Genotyping Console software (version 2.1) based on the BRLMM-P algorithm. We used an ANOVA test to identify SNPs associated with quantitative TRG responses.
2012-12-31 | E-GEOD-35282 | biostudies-arrayexpress
Project description:MiRNA arrays were performed for the plasma exosomes of ESCC patients before treatment. The tumor regression grade of the primary tumor (TRG-PT) was used to evaluate the therapeutic effect of chemoradiotherapy (CRT). Patients classified as Grade 3 were considered sensitive to CRT (n=4), while those classified as Grade 0 or 1a were considered resistant to CRT (n=4).
2022-02-03 | GSE195974 | GEO
Project description:The identification of surrogate single nucleotide polymorphism (SNP) markers that can predict responses to preoperative chemoradiotherapy (CRT) in rectal cancer patients. Genome-wide association studies in clinical populations are theoretically capable of identifying markers that are capable of tumor regression after CRT. We used Affymetrix’s SNP Array 6.0 to detail genetic polymorphism of patient’s group showing differential responsiveness to preoperative CRT and profiled SNP biomarkers.
2012-12-31 | GSE35282 | GEO
Project description:Neoadjuvant chemoradiotherapy (CRT) followed by surgery is the standard treatment for locally advanced rectal cancer (LARC). However, there are no good predictive methods. This study investigated whether specific lncRNA expression is associated with response to CRT. Tissue biopsies were obtained from patients before CRT. LncRNA expression was analyzed using one-color microarrays technique comparing signatures between good respondersand poor responders, as measured by tumour regression grade (TRG).
2020-02-22 | GSE145666 | GEO
Project description:Using Human WG CodeLink microarrays, we established the expression profiling of 26 LARC without metastasis to gain insight into the molecular signatures associated with response to treatment after CRT. The study initially included a total of 35 consecutive patients with locally advanced rectal cancer (LARC) treated at Virgen de las Nieves Hospital from 2008 until 2010. Written informed consent was obtained from all the patients, and the study protocol was approved by the local Clinical Research (Ethics) Committee. They were distributed in two subgroups following a histological classification of response to treatment. Pretherapeutic staging was performed, including complete medical history and physical evaluation, digital rectal examination, endorectal ultrasound, rigid rectoscopy, colonoscopy, PET/TC and chest x-ray. Tumor samples were prospectively obtained during the rectoscopy. All patients subsequently received a total dose of 50.4Gy of radiatio (28 fractions of 1.8Gy) associated with capecitabine or capecitabine and oxaliplatine. Standardized surgery was performed, including total mesorectal excision, after an interval of 8 weeks after chemoradiotherapy. Tumor response was assessed in surgical specimen by semi-quantitative pathological examination (regression grade) including UICC stage. Histopathological tumor regression was graded based on the semiquantitative 5 point tumor regression grading (TRG) system: TRG1 or a TRG2 scores were considered Responders, whereas TRG3, TRG4, and TRG5 scores were classified as Non-Responders. In addition, the tumor regression or radiotherapy effects were assessed by positron emission tomography (18F-FDG PET). Tumor samples of LARC were collected from 35 patients. Nine patients were finally excluded due to the poor quality of the RNA or contradictory results of MandardM-BM-4s criteria and histopathological downstaging, resulting a total of 26 patients. Complete clinical data regarding, age, sex, stage of disease, response to therapy, and overall survival from 26 patients (10 responders and 16 non-responders) was provided in the sample characteristics field. CRT: Chemoradiation; Cap: Capecitabine; Capox: Capecitabine and Oxaliplatine; cTN: clinical stage; Surg: surgical technique; LAR: Low anterior resection; APR: Abdmino-perineal resection; HART: Hartmann, TRG: Tumor Regression Grade; Downst: Downstaging; Downs: downsizing, Resp: response, CPR: complete pathologic response
2014-01-03 | E-GEOD-53781 | biostudies-arrayexpress
Project description:The study objective was to find new biomarkers of treatment response and adverse events in patients receiving neoadjuvant therapy for locally advanced rectal cancer. Patients received neoadjuvant chemotherapy (NACT) followed by chemoradiotherapy (CRT) and underwent treatment evaluation four weeks after CRT completion. Radical pelvic surgery was planned 2-4 weeks later. Patients were scored for treatment adverse events, according to Common Terminology Criteria for Adverse Events (CTCAE) version 3.0, throughout the neoadjuvant treatment course, including at NACT and CRT completion. Treatment response was assessed by histologic ypTN staging and tumor regression grade (TRG) scoring, as well as progression-free survival (time from Inclusion date to Date of local relapse or Date of metastatic disease, whichever came first) recorded for five years after surgery.
2016-04-21 | GSE65622 | GEO
Project description:A total of 97 LARC patients treated at the Institute for Oncology and Radiology of Serbia in the period of 2018-2019 were included in the study. Patients were treated with long-course chemoradiotherapy (CRT): Radiotherapy (RT) was delivered with a total dose of 50.4 Gy in 28 fractions; concomitant chemotherapy (5-FU, 350 mg/m2 daily) and Leucovorin (25 mg/m2 daily) was administered during the first and the fifth week of RT. Patients were evaluated in week 6-8 after treatment completion with pelvic MRI scan and rigid proctoscopy. Pathohistological response after surgery was assessed according to tumor regression grading (TRG) categories by Mandard. Twenty biopsy samples taken at diagnosis were used for proteomic analysis, 9 responders (R, TRG 1-2), and 11 non-responders (NR, TRG 3-5), in order to achieve the maximum range of different molecular features potentially associated with response.
2023-11-21 | PXD040451 | Pride
Project description:Neoadjuvant chemoradiation therapy (CRT) is a widely used preoperative treatment strategy for locally advanced rectal cancer (LARC). However, a few studies have evaluated the molecular changes caused by neoadjuvant CRT in these cancer tissues. Here, we aimed to investigate changes in immunotherapy-related immunogenic effects in response to preoperative CRT in LARC. We analyzed 60 pairs of human LARC tissues before and after irradiation from three independent LARC cohorts, including a LARC patient RNA sequencing (RNA-seq) dataset from our cohort and GSE15781 and GSE94104 datasets. Gene ontology analysis showed that preoperative CRT significantly enriched the immune response in LARC tissues. Moreover, gene set enrichment analysis revealed six significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways associated with downregulated genes, including mismatch repair (MMR) genes, in LARC tissues after CRT in all three cohorts. Radiation also induced apoptosis and downregulated various MMR system-related genes in three colorectal cancer cells. One patient with LARC showed a change in microsatellite instability (MSI) status after CRT, as demonstrated by the loss of MMR protein and PCR for MSI. Moreover, CRT significantly increased tumor mutational burden in LARC tissues. CIBERSORT analysis revealed that the proportions of M2 macrophages and CD8 T cells were significantly increased after CRT in both the RNA-seq dataset and GSE94104. Notably, preoperative CRT increased various immune biomarker scores, such as the interferon-γ signature, the cytolytic activity and the immune signature. Taken together, our findings demonstrated that neoadjuvant CRT modulated the immune-related characteristics of LARC, suggesting that neoadjuvant CRT may enhance the responsiveness of LARC to immunotherapy.
2023-05-31 | GSE233517 | GEO
Project description:The treatment strategy of rectal cancer has substantially changed in recent decades. Historically postoperative chemoradiotherapy (CRT) was considered to be the first-line therapy for stage II and III rectal cancers. However, the preoperative CRT is now considered to be the optimal therapy regimen for locally advanced rectal ancer due to its improved local control, reduced toxicity, and increased rate of sphincter preservation. Our study established a clinically practical multi-class prediction model by adopting a novel strategy that applies two separate prediction models (MI and TO predictor) sequentially to a patient to predict the response. For promising clinical practice, we validated our model in a published dataset, which is completely independent dataset from ours. This study suggests a clinically plausible prediction model that correctly infers the preoperative CRT response of patients with high accuracy based on 163 gene signatures we identified. Total RNAs were isolated from primary rectal tumor tissues of 69 patients who underwent chemoradiation therapy (CRT). These patients are classified into four different CRT responses: minimal response (MI), moderate response (MO), near total response (NT) and total response (TO). All the RNAs were subjected to microarray analysis using Affymetrix GenChip arrays.
2013-05-14 | E-GEOD-46862 | biostudies-arrayexpress