Flux balance analysis predicts Warburg-like effects of mouse hepatocyte deficient in miR-122a

<div><p>The liver is a vital organ involving in various major metabolic functions in human body. MicroRNA-122 (miR-122) plays an important role in the regulation of liver metabolism, but its intrinsic physiological functions require further clarification. This study integrated the genome-scale metabolic model of hepatocytes and mouse experimental data with germline deletion of <i>Mir122a</i> (<i>Mir122a</i>^{<i>–/–</i>}) to infer Warburg-like effects. Elevated expression of <i>MiR-122a</i> target genes in <i>Mir122a</i>^{<i>–/–</i>}mice, especially those encoding for metabolic enzymes, was applied to analyze the flux distributions of the genome-scale metabolic model in normal and deficient states. By definition of the similarity ratio, we compared the flux fold change of the genome-scale metabolic model computational results and metabolomic profiling data measured through a liquid-chromatography with mass spectrometer, respectively, for hepatocytes of 2-month-old mice in normal and deficient states. The <i>Ddc</i> gene demonstrated the highest similarity ratio of 95% to the biological hypothesis of the Warburg effect, and similarity of 75% to the experimental observation. We also used 2, 6, and 11 months of mir-122 knockout mice liver cell to examined the expression pattern of DDC in the knockout mice livers to show upregulated profiles of DDC from the data. Furthermore, through a bioinformatics (LINCS program) prediction, BTK inhibitors and withaferin A could downregulate DDC expression, suggesting that such drugs could potentially alter the early events of metabolomics of liver cancer cells.</p></div

Computational analysis of genomic variants affecting predicted microRNA:target interactions in prostate cancer.

Prostate cancer (PCa) is the most common cancer of men in the United States and is third only to lung and colon as a cause of cancer death. Clinical behavior of the disease is variable and the combination of prostate-specific antigen (PSA) screening and Gleason score staging are currently the best available molecular and pathology tools to predict outcomes. Cancer biology research establishes microRNAs (miRNAs) as key molecular components in both normal and pathological states. Thus, elucidating miRNAs perturbed by genomic alterations will expand our understanding of the molecular taxonomy of PCa with the aim to complement current practices in the diagnosis, prognosis, and treatment of the disease. This study reports the computational analysis of genomic variants affecting the seed sequence of five miRNAs, changing the prediction of microRNA:target interactions in PC3, an androgen-independent cell line that closely resembles prostatic small cell neuroendocrine carcinoma (SCNC). Genomic variants were detected via deep-sequencing of PC3 and further computational work focused on mapping changes within the seed sequence of predicted mature miRNAs. Five microRNA candidates (from now on denominated microRNA*) with changes in the g2-g8 seed region were selected: miR-3161*-5p with rs35834266 G\u3einsA; miR-3620*-5p with rs2070960 C\u3eT; miR-1178*-5p with rs7311975 T\u3eG; miR-4804*-5pwith rs266435 C\u3eG; and miR-449c*-3p with rs35770269 A\u3eT. Subsequently, the computational prediction of miRNA*:target interactions revealed 643 new relationships. After functional enrichment analysis of new targets, seven genes were associated with endocrine resistance (ABCB11, CDKN1B, NOTCH2, SHC4, CCND1, SP1, ADCY2) and five genes with endocrine and other factor regulated calcium reabsorption (ATP1A2, ESR1, PRRKCB, AP2B1, SLC8A1) categories. A gene-disease association literature search was performed for each of the aforementioned genes in order to understand if they have been implicated in cancer, where CDKN1B, NOTCH2, CCND1 have been reported to participate in prostate cancer progression. Microarray gene expression analyses showed that few predicted microRNA* targets were underexpressed in untreated PC3 samples versus prostate epithelial cells from the GEO database. However, after assessing the frequency of observed underexpressed genes per candidate microRNA* using a Fisher’s exact test, miR-4804*-5p target genes (TNKS and GUCY1A3) were statistically significant. Next steps included the comparison between groups of genes subject to non-mutated microRNA and mutated microRNA* regulation using a Kruskal-Wallis non-parametric test. Results were consistent with the microRNA-gene expression regulation model despite the genomic variant in the seed region, nevertheless the effect of miR-3161*-5p, miR-3620*-5p, miR-1178*-5p, miR-4804*-5p, and miR-449c*-3p cannot be predicted solely with the indirect experimental approach that microarray gene expression platforms provide. For this reason, the assessment of recurrent pairwise microRNA-mRNA expression associations was performed using CancerMiner, an online tool from The Cancer Genome Atlas (TCGA) based on a multivariate linear model and rank transformations. Only the relationship of miRNA-3161:CDKN1B was retrieved as a recurrent expression association in uterine corpus endometrial carcinoma (UCEC). In the context of this study, results suggest that CDKN1B (p27Kip1)dysregulation by miR-3161*-5p would be leading to PC3 super proliferation due to the lack of cell cycle arrest from phase G1 to S. Prostate cancer cell line PC3 has shown to share features with prostatic small cell neuroendocrine carcinomas (SCNC) with the implication that molecular mechanisms and therapeutic efficacies observed with PC3 cells are likely applicable to SCNC1. Prostatic small cell neuroendocrine carcinoma is a variant form of prostate cancer often characterized by an aggressive course with a poor response to conventional androgen deprivation therapy (ADT), consistent with the lack of the androgen receptor in prostatic small cell carcinoma (SCC)2. In some men treated with ADT, development of small cell carcinoma might represent the “escape” of a subpopulation of hormone-independent cells resulting from the selective pressure of hormonal therapy3. Hence, the suggestion of CDKN1B dysregulation by miR-3161*-5p might go beyond the idiosyncrasy of the PC3 cell line, but rather an interesting future direction to investigate prostate cancer patients with SCNC rendering to an adverse disease outcome due to uncontrolled cell proliferation