Three exonic variants in the PHEX gene cause aberrant splicing in a minigene assay.

Background: X-linked hypophosphatemia (XLH, OMIM 307800) is a rare phosphorus metabolism disorder caused by PHEX gene variants. Many variants simply classified as missense or nonsense variants were only analyzed at the DNA level. However, growing evidence indicates that some of these variants may alter pre-mRNA splicing, causing diseases. Therefore, this study aimed to use bioinformatics tools and a minigene assay to ascertain the effects of PHEX variations on pre-mRNA splicing. Methods: We analyzed 174 variants in the PHEX gene described as missense or nonsense variants. Finally, we selected eight candidate variants using bioinformatics tools to evaluate their effects on pre-mRNA splicing using a minigene assay system. The complementary DNA (cDNA) sequence for the PHEX gene (RefSeq NM_000444.6) serves as the basis for DNA variant numbering. Results: Of the eight candidate variants, three were found to cause abnormal splicing. Variants c.617T>G p.(Leu206Trp) and c.621T>A p.(Tyr207*) in exon 5 altered the splicing of pre-mRNA, owing to the activation of a cryptic splice site in exon 5, which produced an aberrant transcript lacking a part of exon 5, whereas variant c.1700G>C p.(Arg567Pro) in exon 16 led to the activation of a cryptic splice site in intron 16, resulting in a partial inclusion of intron 16. Conclusion: Our study employed a minigene system, which has a great degree of flexibility to assess abnormal splicing patterns under the circumstances of patient mRNA samples that are not available, to explore the impact of the exonic variants on pre-mRNA splicing. Based on the aforementioned experimental findings, we demonstrated the importance of analyzing exonic variants at the mRNA level.

A novel decision tree model based on chromosome imbalances in cell-free DNA and CA-125 in the differential diagnosis of ovarian cancer.

OBJECTIVE: CA-125 is widely used as biomarker of ovarian cancer. However, CA-125 suffers low accuracy. We developed a hybrid analytical model, the Ovarian Cancer Decision Tree (OCDT), employing a two-layer decision tree, which considers genetic alteration information from cell-free DNA along with CA-125 value to distinguish malignant tumors from benign tumors. METHODS: We consider major copy number alterations at whole chromosome and chromosome-arm level as the main feature of our detection model. Fifty-eight patients diagnosed with malignant tumors, 66 with borderline tumors, and 10 with benign tumors were enrolled. RESULTS: Genetic analysis revealed significant arm-level imbalances in most malignant tumors, especially in high-grade serous cancers in which 12 chromosome arms with significant aneuploidy (P<0.01) were identified, including 7 arms with significant gains and 5 with significant losses. The area under receiver operating characteristic curve (AUC) was 0.8985 for copy number variations analysis, compared to 0.8751 of CA125. The OCDT was generated with a cancerous score (CScore) threshold of 5.18 for the first level, and a CA-125 value of 103.1 for the second level. Our most optimized OCDT model achieved an AUC of 0.975. CONCLUSIONS: The results suggested that genetic variations extracted from cfDNA can be combined with CA-125, and together improved the differential diagnosis of malignant from benign ovarian tumors. The model would aid in the pre-operative assessment of women with adnexal masses. Future clinical trials need to be conducted to further evaluate the value of CScore in clinical settings and search for the optimal threshold for malignancy detection.

NHE1 Mediates 5-Fu Resistance in Gastric Cancer via STAT3 Signaling Pathway.

BACKGROUND: Several recent studies have addressed the role of Na+/H+ exchanger isoform 1 (NHE1) in tumor cell growth and apoptosis, including in gastric cancer. However, the role of NHE1 expression related to the 5-Fu resistance in gastric cancer has not been investigated. METHODS: The expression of NHE1 was examined by qPCR in the SGC7901/5-FU cell line and its parental cell line. pcDNA3.1-NHE1 and NHE1-siRNA were transfected to SGC7901/5-FU resistance cells and cell apoptosis was detected via TUNEL assay. The upstream activators in NHE1 mediated 5-Fu resistant gastric cancer cells were detected by Western blot and immunofluorescent. RESULTS: A significant increase of the expression of NHE1 was observed in SGC7901 5-FU resistance cells compared to the GES-1 and SGC7901 cell line. NHE1 can suppress the cell apoptosis of SGC7901 5-FU resistance cells and involved in cell cycle. Also, the migration and invasion of SGC7901 5-FU resistance cells were promoted by NHE1. NHE1 also increases the intracellular pH. The results of Western blot analysis showed that NHE1 overexpression induced an increase in the expression of phosphorylated activator transcription factor 3 (pSTAT3). The more obvious phosphorylated level was shown in the phosphorylated STAT3 at pSTAT3tyr705. Further investigations revealed that the constitutive activation of STAT3 may be induced by JAK1 and JAK2, and thus effect the 5-FU resistance by regulating NHE1. DISCUSSION: In summary, our findings provided evidence that NHE1 contributed to 5-Fu resistance in gastric cancer cells by regulating the JAK/STAT3 pathway. Therefore, NHE1 can be a useful marker for predicting and monitoring 5-Fu resistance.