The Prognostic Value of ASPHD1 and ZBTB12 in Colorectal Cancer: A Machine Learning-Based Integrated Bioinformatics Approach.

Introduction: Colorectal cancer (CRC) is a common cancer associated with poor outcomes, underscoring a need for the identification of novel prognostic and therapeutic targets to improve outcomes. This study aimed to identify genetic variants and differentially expressed genes (DEGs) using genome-wide DNA and RNA sequencing followed by validation in a large cohort of patients with CRC. Methods: Whole genome and gene expression profiling were used to identify DEGs and genetic alterations in 146 patients with CRC. Gene Ontology, Reactom, GSEA, and Human Disease Ontology were employed to study the biological process and pathways involved in CRC. Survival analysis on dysregulated genes in patients with CRC was conducted using Cox regression and Kaplan-Meier analysis. The STRING database was used to construct a protein-protein interaction (PPI) network. Moreover, candidate genes were subjected to ML-based analysis and the Receiver operating characteristic (ROC) curve. Subsequently, the expression of the identified genes was evaluated by Real-time PCR (RT-PCR) in another cohort of 64 patients with CRC. Gene variants affecting the regulation of candidate gene expressions were further validated followed by Whole Exome Sequencing (WES) in 15 patients with CRC. Results: A total of 3576 DEGs in the early stages of CRC and 2985 DEGs in the advanced stages of CRC were identified. ASPHD1 and ZBTB12 genes were identified as potential prognostic markers. Moreover, the combination of ASPHD and ZBTB12 genes was sensitive, and the two were considered specific markers, with an area under the curve (AUC) of 0.934, 1.00, and 0.986, respectively. The expression levels of these two genes were higher in patients with CRC. Moreover, our data identified two novel genetic variants-the rs925939730 variant in ASPHD1 and the rs1428982750 variant in ZBTB1-as being potentially involved in the regulation of gene expression. Conclusions: Our findings provide a proof of concept for the prognostic values of two novel genes-ASPHD1 and ZBTB12-and their associated variants (rs925939730 and rs1428982750) in CRC, supporting further functional analyses to evaluate the value of emerging biomarkers in colorectal cancer.

Association study of a single nucleotide polymorphism in brain cytoplasmic 200 long-noncoding RNA and psychiatric disorders.

The Brain cytoplasmic 200 RNA (BC200 RNA) is neuron-specific lncRNA with putative roles in normal aging and in the pathogenesis of Alzheimer's disease. Its role in the neuron plasticity has also been documented. In the current study, we genotyped a single nucleotide polymorphism (SNP) within this lncRNA (rs4404327) in a population of Iranian patients with diverse neuropsychiatric conditions including substance addiction (n = 315), attention deficit hyperactive disorder (ADHD) (n = 53), bipolar 1 (BP1) (n = 131), bipolar 2 (BP2) (n = 68), major depressive disorder (MDD) (n = 56) and schizophrenia (SCZ) (n = 177) as well as age-/ sex-matched healthy controls. This SNP was associated with ADHD in co-dominant model (C/T vs. C/C) (OR (95% CI) = 3.7 (1.96-10), P value = 0.000193), dominant model (C/T + T/T vs. C/C) (OR (95% CI) = 4.43(2.02-9.72), P value = 1.37E-04) and multiplicative model (C vs. T) (OR (95% CI) = 3.20(1.64-6.25), P value = 4.316269E-04). Moreover, this SNP was associated with risk of BP1 in dominant model (OR (95% CI) = 1.67(1.08-2.62), P value = 0.02) and multiplicative model (OR (95% CI) = 1.51 (1.04-2.21), P value = 0.028). After correction for multiple comparisons (6 cohorts × 4 models), associations remained significant in ADHD but not in BP1. No other significant association was detected. The current project showed association between a certain SNP within BC200 RNA and ADHD. Further studies are required to assess these associations in larger cohorts of patients and find the underlying mechanism for this observation.

A Single Nucleotide Polymorphism in GAS5 lncRNA is Associated with Risk of Bladder Cancer in Iranian Population.

Down-regulation of the long non-coding RNA (lncRNA) growth arrest-specific 5 (GAS5) has a pathogenic role in bladder cancer. Moreover, genomic variants of this lncRNA have been associated with risk of diverse cancers. In the present project, we genotyped two putative functional SNPs (rs2067079 and rs6790) in 122 bladder cancer patients and 150 age- and sex-matched healthy subjects. The rs2067079 was associated risk of bladder cancer in recessive inheritance model (TT vs.CC + CT: OR (95% Confidence interval (CI)) = 2.67 (1.27-5.62), adjusted P value = 0.02). The T G haplotype (rs2067079 and rs6790) increased the risk of bladder cancer in the assessed population (OR (95% CI) = 1.73 (1.18-2.56), adjusted P value = 0.02). Consequently, in the current project we introduced a novel risk locus for bladder cancer in Iranian population.

ANRIL Variants Are Associated with Risk of Neuropsychiatric Conditions.

The antisense non-coding RNA in the INK4 locus (ANRIL) is a long non-coding RNA (lncRNA) whose contribution in several human disorders has been verified. In the current projects, we genotyped two single nucleotide polymorphisms (SNPs) in this lncRNA (rs1333045 and rs1333048) in a population of Iranian patients with bipolar disorder (BP), major depressive disorder (MDD), and methamphetamine addiction. The rs1333045 was associated with methamphetamine addiction in recessive and multiplicative models (OR (95% CI) = 1.867 (1.211-2.877), adjusted p value = 8.75E-03 and OR (95% CI) = 1.415 (1.089-1.839), adjusted p value = 1.87E-02 respectively). The rs1333048 was associated with methamphetamine addiction in co-dominant model (A/A vs. C/C: OR (95% CI) = 0.195 (0.114-0.336), adjusted p value = 2.44E-09) and in other inheritance models. The rs1333045 was not associated with risk of BP I in any inheritance model. However, the rs1333048 was associated with BP I in co-dominant model (A/A vs. C/C: OR (95% CI) = 0.499 (0.286-0.870), adjusted p value = 2.53E-07) and in other inheritance models. In BP II cohort, we detected significant associations between both SNPs and risk of disorder in all inheritance models. In co-dominant model, these associations were detected just between homozygotes (T/T vs. C/C (rs1333045); A/A vs. C/C and (rs1333048)). The rs1333045 was associated with MDD in recessive model (OR (95% CI) = 2.221 (1.173-4.207), adjusted p value = 0.026). The rs1333048 was associated with MDDs in dominant, recessive, and multiplicative models. The selected SNPs were not in linkage disequilibrium (D' statistic = 0.23, r2 = 0.05). Haplotype analyses have shown that T A haplotype block (rs1333045 and rs1333048 respectively) significantly decreases risk of addiction, BP I, BP II, and MDD. Besides, the C C haplotype decreases risk of addiction, BP II and MDD. Finally, the T C haplotype increases risk of BP I, BP II, and MDD. Based on the above-mentioned data, the selected ANRIL SNPs or other SNPs in linkage disequilibrium with them might confer risk of neuropsychiatric disorders. Taken together, ANRIL can be regarded as a risk locus for these conditions.

Downregulation of nicotinamide nucleotide transhydrogenase and its naturally occurring antisense RNA in gastric cancer.

AIM: Nicotinamide Nucleotide Transhydrogenase (NNT) gene encodes a protein, which is an important antioxidative enzyme that converts NADH to NADPH. This enzyme provides a significant proportion of the entire NADPH resource in the mitochondria. Previous reports have shown possible contribution of this gene in the carcinogenesis process. METHODS: In the current research, we evaluated expression levels of NNT gene and a naturally occurring antisense RNA (NNT-AS1) in gastric cancer specimens compared to their corresponding adjacent noncancerous tissues (ANCTs). RESULTS: Both NNT1 and NNT-AS1 genes were significantly downregulated in tumor tissues compared to ANCTs (expression ratio = 0.369, p = .045 and expression ratio = 0.368, p = .043, respectively). Transcript levels of NNT1 and NNT-AS1 were associated with the location of the primary tumor (p = .003 and .002, respectively). Moreover, expressions of both genes were significantly elevated in tumors with lymphatic/vascular invasion compared to tumors without lymphatic/vascular invasion (p = .001 and p = .005). No other remarkable associations were noticed between transcript levels of genes in tumor tissues and patients' information. Based on the area under curve (AUC) values in the receiver operating characteristic (ROC) curves, the diagnostic power of NNT1 and NNT-AS1 were estimated to be 0.62 and 0.63, respectively. CONCLUSIONS: Although we demonstrated dysregulation of NNT1 and NNT-AS1 in gastric tumor specimens in association with clinical data of patients, these two genes are not supposed to be appropriate biomarkers for gastric cancer.

Brain-derived neurotrophic factor downregulation in gastric cancer.

The brain-derived neurotrophic factor (BDNF) is a certain type of growth factor that participates in the correct construction of the brain. Moreover, some reports have shown its participation in the tumorigenesis process. A long noncoding RNA known as BDNF-antisense (BDNF-AS) is shown to be transcribed from the antisense direction of the BDNF gene and control its expression. In the current study, we compared expression levels of BDNF and its antisense in gastric cancer tissues and adjacent noncancerous tissues (ANCTs) using quantitative real-time polymerase chain reaction. Expression of both genes tended to decrease in gastric cancer tissues in comparison with ANCTs (expression ratio = 0.4 and P = .06 for BDNF; expression ratio = 0.35 and P = .05 for BDNF-AS, respectively). Relative transcript levels of both genes were remarkably associated with the site of primary tumor in a way that all cardia tumors had low levels of both BDNF and BDNF-AS in comparison with their paired ANCTs (P = .002 and P = <.001). We also found higher amounts of both genes in malignant samples obtained from older patients (P = .01 and P = .03 for BDNF and BDNF-AS, respectively). Besides, BDNF expression was higher in tumors with lymphatic/vascular invasion (P = .01). There was also a trend toward upregulation of BDNF-AS in tumors with lymphatic/vascular invasion (P = .05). The current study underscores the role of BDNF and BDNF-AS in the pathogenic process leading to gastric cancer.