Dataset Information

Design, optimization and validation of genes commonly used in expression studies on DMH/AOM rat colon carcinogenesis model.

ABSTRACT: Colorectal cancer (CRC), also known as colon cancer, is the third most common form of cancer worldwide in men and the second in women and is characterized by several genetic alterations, among them the expression of several genes. 1,2-dimethylhydrazine (DMH) and its metabolite azoxymethane (AOM) are procarcinogens commonly used to induce colon cancer in rats (DMH/AOM rat model). This rat model has been used to study changes in mRNA expression in genes involved in this pathological condition. However, a lack of proper detailed PCR primer design in the literature limits the reproducibility of the published data. The present study aims to design, optimize and validate the qPCR, in accordance with the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines, for seventeen genes commonly used in the DMH/AOM rat model of CRC (Apc, Aurka, Bax, Bcl2, ?-catenin, Ccnd1, Cdkn1a, Cox2, Gsk3beta, IL-33, iNOs, Nrf2, p53, RelA, Smad4, Tnf? and Vegfa) and two reference genes (Actb or ?-actin and B2m). The specificity of all primer pairs was empirically validated on agarose gel, and furthermore, the melting curve inspection was checked as was their efficiency (%) ranging from 90 to 110 with a correlation coefficient of r 2 > 0.980. Finally, a pilot study was performed to compare the robustness of two candidate reference genes.

SUBMITTER: Bars-Cortina D

PROVIDER: S-EPMC6357868 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Design, optimization and validation of genes commonly used in expression studies on DMH/AOM rat colon carcinogenesis model.

Bars-Cortina David D Riera-Escamilla Antoni A Gou Gemma G Piñol-Felis Carme C Motilva María-José MJ

PeerJ 20190129

Colorectal cancer (CRC), also known as colon cancer, is the third most common form of cancer worldwide in men and the second in women and is characterized by several genetic alterations, among them the expression of several genes. 1,2-dimethylhydrazine (DMH) and its metabolite azoxymethane (AOM) are procarcinogens commonly used to induce colon cancer in rats (DMH/AOM rat model). This rat model has been used to study changes in mRNA expression in genes involved in this pathological condition. How ...[more]

PMID: 30713822

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Project description:BACKGROUND:Patient-reported outcome measures (PROMs) have become widely adopted in the care of patients with prostate cancer, but there is no validated crosswalk between two commonly used instruments, the Expanded Prostate Cancer Index Composite Short Form (EPIC-26) and the Memorial Sloan Kettering (MSK) instrument, which consists of the International Index of Erectile Function-6 (IIEF-6) questionnaire and the MSK radical prostatectomy urinary outcome scale. OBJECTIVE:To develop and validate bidirectional crosswalks between the sexual and urinary domains (single domain in MSK, separate incontinence and irritative/obstructive domains in EPIC-26) of the MSK and EPIC-26 instruments. DESIGN, SETTING, AND PARTICIPANTS:Radical prostatectomy (RP) patients completing instruments at MSK and Michigan Urological Surgery Improvement Collaborative (MUSIC) between January and May of 2017 were invited to enroll. Stratified random sampling (by institution, MSK urinary function score, and MSK erectile function score) was used to divide patient data into training and test sets. Models were developed to predict the domain score for each instrument using the other's item responses and domain scores. Performance was evaluated using capped root-mean-squared error and accuracy at established thresholds. RESULTS AND LIMITATIONS:We received 517 instruments at MSK and 1033 within MUSIC, which were assigned to training (825), post-RP test (412), and pre-RP test (313) sets. We found the crosswalks to have low error and high accuracy. Although the crosswalks are more accurate if responses to each item are known, it is possible to convert between instruments on the basis of a total domain score. CONCLUSIONS:The crosswalks are a valid way to convert between sexual and urinary domains of the MSK and EPIC-26 instruments. PATIENT SUMMARY:We developed and validated a set of formulas that allow conversion of sexual and urinary function scores between the Memorial Sloan Kettering and Expanded Prostate Cancer Index Composite Short Form patient-reported outcome questionnaires. These crosswalks allow seamless transition between the two questionnaires.

Dataset Information

Design, optimization and validation of genes commonly used in expression studies on DMH/AOM rat colon carcinogenesis model.

Publications

Design, optimization and validation of genes commonly used in expression studies on DMH/AOM rat colon carcinogenesis model.

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