Transcriptome analysis of colorectal cancer liver metastasis: The importance of long non-coding RNAs and fusion transcripts in the disease pathogenesis.

BACKGROUND: Despite several attempts to define the many genomic aspects of colorectal cancer liver metastasis (CRC-LM), there is still a lack of a complete and accurate picture of the cancer transcriptome and its function in the generation of metastasis. METHODS: Cancer Genome Atlas Sequence Read Archive (SRA) was used to get RNA sequencing data for CRC-LM and primary CRC. The CDseqR deconvolution method followed by the edgeR statistical approach was employed to accurately find differentially expressed genes (DEGs). Weighted gene co-expression network analysis (WGCNA) was used to determine the long non-coding RNA (lncRNA) and mRNA pairs in CRC-LM etiology. Three alternative methods were used to explore fusion transcripts to anticipate the potential driver chimeras. RESULTS: Multiple cancer-related pathways were enriched in the up-regulated genes, including cell cycle, DNA replication, and RNA transport. SPP1 was the most up-regulated gene important in the cellular proliferation and migration and CCDC152 was the most down-regulated gene known in the metastatic spread of CRC. There were seven distinct lncRNAs discovered, two of which were novel (LOC107984834 and LOC107985040) and associated with metastatic related pathways such as the extracellular matrix-receptor interaction. Overall survival analysis demonstrated that SPP1 and LOC107985040 were significantly associated with poor prognosis outcomes. Seven new fusion transcripts were found in seven CRC-LM patients (22.5%) anticipated to have potential driver functions in cancer. CONCLUSION: The newly discovered dysregulated genes and other transcriptome abnormalities could contribute to a better understanding of the CRC-LM underlying mechanism, leading to the development of new diagnostic, prognostic, and therapeutic molecular options for personalized medicine.

Simple and cost-effective laboratory methods to evaluate and validate cell-free DNA isolation.

OBJECTIVE: In the present study, we investigated different simple and cost effective methods to evaluate and validate cell free DNA (cfDNA) isolation. The ability of the QIAamp DNA Blood Mini Kit method to extract cfDNA was assessed by several approaches, including purification of endogenous cfDNA and exogenous spike-in control material, prior to plasma extraction, and followed by quantitative-PCR. RESULTS: Using QIAamp DNA Blood Mini kit, nearly 27% (380 bp) to 35% (173 bp) cfDNA was recovered with a higher recovery of smaller size cfDNA (173 bp) in comparison to larger ones (380 bp). These simple laboratory methods can be used to assess the efficiency of any cfDNA isolation method.

BMP3 promoter hypermethylation in plasma-derived cell-free DNA in colorectal cancer patients.

Detecting cfDNA in plasma or serum could serve as a 'liquid biopsy', for circulating tumor DNA with aberrant methylation patterns offer a possible method for early detection of several cancers which could avoid the need for tumor tissue biopsies. Bone Morphogenetic Protein 3 (BMP3) was identified as a candidate tumor suppressor gene putatively down-regulated in colorectal cancer (CRC). In this study, we aimed to assess the potential role of BMP3 promoter methylation changes in plasma DNA for detection of colorectal cancerous and precancerous lesions. Plasma DNA samples were extracted from 50 patients with histologically diagnosed polyps or tumor and 50 patients reported negative for polyps or tumors. The procedure consists of bisulfite conversion of the extracted DNA, purification of bis-DNA, and BMP3 methylation status analysis by using the bisulfite specific high resolution melting analysis. This study demonstrated that there was a significantly higher frequency of BMP3 methylated DNA in plasma in patients with polyps versus healthy controls with a sensitivity and specificity of 40 and 94%, respectively. In conclusion, our results demonstrated that BMP3 DNA methylation in plasma had not have sufficient sensitivity and it should be used in combination with other biomarkers for the detection of CRC.

Examine the Relationship between Mindfulness and Drug Craving in Addicts Undergoing Methadone Maintenance Treatment.

BACKGROUND: The aim of this study was examination the relationship between mindfulness and drug craving in addicts undergoing methadone maintenance treatment. METHODS: The subjects of this research were 80 addicts undergoing methadone maintenance treatment selected through available sampling from four addiction treatment center in Ahvaz from March 2012 to September 2012. Two questionnaires to examine the variables of this study were the five facets mindfulness questionnaire (FFMQ) and hero-in craving questionnaire (HCQ). The data were analyzed using SPSS version 16. RESULTS: The Pearson correlational results indicated significant reverse relation between mindfulness factors and craving sub scales (P<0.05). Besides, the regression results indicated that four factors of mindfulness such as observation, describing, acting with awareness and non-reactivity to inner experience can totally predict 48 percent of craving variance (P<0.01 ). CONCLUSION: There is a reverse relation between mindfulness and craving. Therefore we advise the researchers in addiction fields that in line with various studies that indicated effectiveness of mindfulness based interventions in improving various psychological problems, be researcher in effectiveness of this intervention in addiction fields. Moreover, we advise the addiction therapists to use mindfulness based interventions and technics in order to reduction of emotional and cognitive problems co morbidities with addiction such as craving that is one of potential factors affecting survival and relapse to drug abuse.

Comparison of General Well-being of Patients Undergoing Methadone Maintenance Therapy (MMT) with Patients Undergoing Naltrexone Therapy.

BACKGROUND: Drug abuse is a problem that causes a wide array of social, emotional, and physical problems and involves both patients and the society. Helping the addicted has always been a priority for physicians and especially psychiatrists. The purpose of this prospective study was to compare the effects of methadone and naltrexone in general well-being of patients undergoing these treatments. METHODS: Forty-six patients who were taking either methadone or naltrexone were selected and evaluated for a period of 5 months using a 28-item questionnaire about their general health. RESULTS: In spite of the fact that patients undergoing methadone treatment had more severe symptoms and prognoses regarding their age, duration of drug abuse, and number of treatment attempts, these patients showed better general health and social functioning comparing to patients undergoing naltrexone treatment during the 6-month period of this study (P<0.000). CONCLUSION: Methadone might be regarded as an effective and useful medicine in treatment of addiction.