Targeting Splicing Factor SRSF6 for Cancer Therapy

Aberrant alternative splicing of pre-mRNA is an emerging cancer hallmark. Many cancer-associated genes undergo alternative splicing to produce multiple isoforms with diverse or even antagonistic functions. Oncogenic isoforms are often up-regulated, whereas tumor suppressive isoforms are down-regulated during tumorigenesis. Serine/arginine-rich splicing factor 6 (SRSF6) is an important splicing factor that regulates the alternative splicing of hundreds of target genes, including many cancer-associated genes. The potential roles of SRSF6 in cancers have attracted increasing attentions in the past decade. Accumulated pieces of evidence have shown that SRSF6 is a potential oncogenic gene that promotes oncogenic splicing when overexpressed. Targeting SRSF6 may suppress tumorigenesis. In this review, we describe the gene, mRNA, and protein structure of SRSF6; summarize the current understanding of the expression, functions, and regulatory mechanisms of SRSF6 during tumorigenesis; and discuss the potential application of targeting SRSF6 in cancer treatment.

Development of transcriptomics-based eukaryotes growth rate indices

Growth rate estimation is important to understand the flow of energy and nutrient elements in an ecosystem, but it has remained challenging, especially on microscopic organisms. In this study, we propose four growth rate indices that use mRNA abundance ratios between nuclear and mitochondrial genes: (1) total nuclear and mitochondrial mRNA ratio (Nuc:Mito-TmRNA), (2) nuclear and mitochondrial ribosomal protein mRNA ratio (Nuc:Mito-RPmRNA), (3) gene ontology (GO) terms and total mitochondrial mRNA ratios and (4) nuclear and mitochondrial specific gene mRNA ratio. We examine these proposed ratios using RNA-Seq datasets of Daphnia magna and Saccharomyces cerevisiae. The results showed that both Nuc:Mito-TmRNA and Nuc:Mito-RPmRNA ratio indices showed significant correlations with the growth rate for both species. A large number of GO terms mRNA ratios showed significant correlations with the growth rate of S. cerevisiae. Lastly, we identified mRNA ratios of several specific nuclear and mitochondrial gene pairs that showed significant correlations. We foresee future implications for the proposed mRNA ratios used in metatranscriptome analyses to estimate the growth rate of communities and species.

Pomegranate Extract (POMx) Induces Mitochondrial Dysfunction and Apoptosis of Oral Cancer Cells

The anticancer effect of pomegranate polyphenolic extract POMx in oral cancer cells has rarely been explored, especially where its impact on mitochondrial functioning is concerned. Here, we attempt to evaluate the proliferation modulating function and mechanism of POMx against human oral cancer (Ca9-22, HSC-3, and OC-2) cells. POMx induced ATP depletion, subG1 accumulation, and annexin V/Western blotting-detected apoptosis in these three oral cancer cell lines but showed no toxicity to normal oral cell lines (HGF-1). POMx triggered mitochondrial membrane potential (MitoMP) disruption and mitochondrial superoxide (MitoSOX) generation associated with the differential downregulation of several antioxidant gene mRNA/protein expressions in oral cancer cells. POMx downregulated mitochondrial mass, mitochondrial DNA copy number, and mitochondrial biogenesis gene mRNA/protein expression in oral cancer cells. Moreover, POMx induced both PCR-based mitochondrial DNA damage and γH2AX-detected nuclear DNA damage in oral cancer cells. In conclusion, POMx provides antiproliferation and apoptosis of oral cancer cells through mechanisms of mitochondrial impairment.

Prospective validation of an 11-gene mRNA host response score for mortality risk stratification in the intensive care unit

Several clinical calculators predict intensive care unit (ICU) mortality, however these are cumbersome and often require 24 h of data to calculate. Retrospective studies have demonstrated the utility of whole blood transcriptomic analysis in predicting mortality. In this study, we tested prospective validation of an 11-gene messenger RNA (mRNA) score in an ICU population. Whole blood mRNA from 70 subjects in the Stanford ICU Biobank with samples collected within 24 h of Emergency Department presentation were used to calculate an 11-gene mRNA score. We found that the 11-gene score was highly associated with 60-day mortality, with an area under the receiver operating characteristic curve of 0.68 in all patients, 0.77 in shock patients, and 0.98 in patients whose primary determinant of prognosis was acute illness. Subjects with the highest quartile of mRNA scores were more likely to die in hospital (40% vs 7%, p < 0.01) and within 60 days (40% vs 15%, p = 0.06). The 11-gene score improved prognostication with a categorical Net Reclassification Improvement index of 0.37 (p = 0.03) and an Integrated Discrimination Improvement index of 0.07 (p = 0.02) when combined with Simplified Acute Physiology Score 3 or Acute Physiology and Chronic Health Evaluation II score. The test performed poorly in the 95 independent samples collected > 24 h after emergency department presentation. Tests will target a 30-min turnaround time, allowing for rapid results early in admission. Moving forward, this test may provide valuable real-time prognostic information to improve triage decisions and allow for enrichment of clinical trials.

miR-208b Regulates Rabbit Preadipocyte Proliferation and Differentiation

microRNAs (miRNAs) play an important role in gene regulation in animals by pairing with target gene mRNA. Many miRNAs are differentially expressed in the adipose tissue, often with conserved expression. In our study, we found that miR-208b expression was observed differently in the preadipocyte differentiation model. When miR-208b was overexpressed in the preadipocyte differentiation model, the overexpressed group displayed higher expression of PPARγ and FABP4—the markers of preadipocyte differentiation. Oil Red O staining revealed that the count of lipid droplets was increased in the overexpressed group. When the expression of miR-208b was inhibited, the above indicators showed an opposite trend. Moreover, results from both 5-ethynyl-2’-deoxyuridine (EDU) and cell counting kit (CCK) analysis showed that miR-208b promoted the proliferation of preadipocyte. Expression of gene CSNK2A2, a direct miR-208b target, was downregulated in the overexpressed group, providing a possible link to multiple signal pathways. Overall, our data indicate that miR-208b play a positive regulatory effect on the proliferation and differentiation of rabbit preadipocyte.

Development of a method for the determination of the JAK2 gene mRNA in venous blood and assessment of its diagnostic value in oncohematology

Overactive JAK pathway signaling is a hallmark of immune diseases and critically affects on inflammation and coagulation. A number of mutations in the JAK2 gene act as driving forces of myeloproliferative neoplasms (MPN), the pathogenesis of certain variants of acute leukemia, a number of solid malignancies and cardiovascular diseases. Assays for quantifying JAK2 mRNA in circulating blood cells can be used as a marker associated with the activity of this enzyme. Development of an original method for detecting JAK2 mRNA in venous blood and assessment of the possible diagnostic value in chronic oncohematological diseases. The development of an RT-PCR method for determining the expression of the JAK2 gene mRNA in venous blood samples was carried out in accordance with the MIQE requirements. Primers and TaqMan probes were designed using the Primer3 program, taking into account the possibility of excluding subsequent DNase treatment. The stability of the investigated mRNA was assessed in vacutainers with different anticoagulants and depending on the storage time of the samples. The study of the expression of JAK2 mRNA in blood leukocytes of 41 patients with B-CLL, 16 patients with CML, 12 patients with multiple myeloma and 39 donors using the developed “real-time” PCR method. The study revealed a decrease in the level of JAK2 mRNA in venous blood samples in patients with primary CLL, but not with CML or with multiple myeloma. The level of the marker in the majority of patients with CLL after the start of therapy returned to the range typical for healthy people. It has been shown that the values of the relative expression of JAK2 mRNA are most stable in the range of 2 - 7 hours after taking blood in a vacutainer with EDTA. An original RT-PCR method was developed for the quantitative determination of JAK2 mRNA in venous blood samples, which meets the requirements of the MIQE system. Determination of JAK2 mRNA can be useful for clarifying the pathogenesis features of certain diseases involving impaired Janus kinase activity and can become a promising marker for prognosis and assessment of the effectiveness of therapy.

Identification of four insertion sites for foreign genes in a pseudorabies virus vector

Background Pseudorabies virus (PRV) is a preferred vector for recombinant vaccine construction. Previously, we generated a TK&gE-deleted PRV (PRVΔTK&gE−AH02) based on a virulent PRV AH02LA strain. It was shown to be safe for 1-day-old piglets with maternal PRV antibodies and 4 ~ 5 week-old PRV antibody negative piglets and provide rapid and 100 % protection in weaned pigs against lethal challenge with the PRV variant strain. It suggests that PRVTK&gE−AH02 may be a promising live vaccine vector for construction of recombinant vaccine in pigs. However, insertion site, as a main factor, may affect foreign gene expression. Results In this study, we constructed four recombinant PRV-S bacterial artificial chromosomes (BACs) carrying the same spike (S) expression cassette of a variant porcine epidemic diarrhea virus strain in different noncoding regions (UL11-10, UL35-36, UL46-27 or US2-1) from AH02LA BAC with TK, gE and gI deletion. The successful expression of S gene (UL11-10, UL35-36 and UL46-27) in recombinant viruses was confirmed by virus rescue, PCR, real-time PCR and indirect immunofluorescence. We observed higher S gene mRNA expression level in swine testicular cells infected with PRV-S(UL11-10)ΔTK/gE and PRV-S(UL35-36)ΔTK/gE compared to that of PRV-S(UL46-27)ΔTK/gE at 6 h post infection (P < 0.05). Moreover, at 12 h post infection, cells infected with PRV-S(UL11-10)ΔTK/gE exhibited higher S gene mRNA expression than those infected with PRV-S(UL35-36)ΔTK/gE (P = 0.097) and PRV-S(UL46-27)ΔTK/gE (P < 0.05). Recovered vectored mutant PRV-S (UL11-10, UL35-36 and UL46-27) exhibited similar growth kinetics to the parental virus (PRVΔTK&gE−AH02). Conclusions This study focuses on identification of suitable sites for insertion of foreign genes in PRV genome, which laids a foundation for future development of recombinant PRV vaccines.

The Effect of a Novel Glucocorticoid Receptor Antagonist (CORT113176) on Glucocorticoid and Insulin Receptor Sensitive Hepatic Gene (mRNA) Expression in a Neonatal Rat Model of Human Prematurity

Preterm birth is a global health problem the sequelae of which are not well understood. Hypoxia, a common stressor with prematurity, can affect blood glucose via stress-induced increases in glucocorticoids (GC). GCs are also administered to preterm infants to improve oxygenation; however, this is controversial. CORT113176 (Corcept Therapeutics) is a novel, selective glucocorticoid receptor (GR) antagonist that does not bind to the progesterone receptor. We have demonstrated that CORT113176 (in our rat model of preterm birth) increases baseline corticosterone (due to loss of GC negative feedback) and attenuates hypoxia-induced increases in insulin resistance implicating endogenous corticosterone in post-natal metabolic adaptations to stress. We now propose that CORT113176 is useful to evaluate the hepatic effects of endogenous GCs in our rat model of preterm birth by measuring critical GC and insulin receptor sensitive gene mRNAs. Postnatal day (PD) 2 rat pups of both sexes (N=5 per treatment/sex) were pretreated with CORT113176 (600 mg/kg IP) or vehicle. After 60 minutes, a group of pups were euthanized with livers collected and preserved in RNAlater (baseline). The remaining pups were separated from their dams, exposed to normoxia (control) or hypoxia (8% O2) for 60 minutes, and livers obtained. Total hepatic RNA was extracted, and mRNA expression was analyzed (RT-qPCR) for GC and insulin receptor sensitive genes: GC: Fkbp5, Gilz, Nr3c1 (Gr), Nr3c2 (Mr), Per1, Ttpa. INSULIN: Akt2, G6Pase, Igf1r, Insr, Irs1, Irs2, Pik3cb, Pik3r1, Srebp1c. CORT113176 decreased the expression of all baseline hepatic insulin receptor mRNAs in both sexes, except for G6Pase. Pik3r1 mRNA expression significantly decreased with 60 minutes of normoxic separation (fasting) in males and females compared to baseline and hypoxic separation; this was blocked by CORT113176. In the GC receptor sensitive panel, CORT113176 decreased basal Nr3c1 (Gr) mRNA. Normoxic and hypoxic separation increased Per1 and Gilz mRNA expression; this effect was blocked by CORT113176. Interestingly, Fkbp5 expression, a proposed clinical marker for GR antagonism, was not altered by CORT113176. The hepatic GC and insulin receptor sensitive gene mRNA panels we developed are sensitive to GR antagonism suggesting they may be a useful addition to Fkbp5. The increase in endogenous corticosterone, acting via GR, is critical in the hepatic response to stress in our neonatal rat model of hypoxia and prematurity.

Quercetin and a plant substance, identified using a multi-copy number of DNA topoisomerase I in recombinant Pichia pastoris, inhibited MDA-MB-231 proliferation via different manners.

The study employed an in vivo strategy to construct a multi-copy number of human DNA topoisomerase I (hTopI) gene using pPIC3.5K vector in GS115 strain of Pichia. The yeast transformant (GS115-pPIC3.5K-hTopI; clone) was then used to investigate the preliminary growth effect of a pure compound (quercetin) and a standardised subfraction of ethanolic red onion peel extract (F1). The clones’ cell density was likely to be unaffected; only the total protein expression and enzyme activity were increased following the increased copy number of hTop1 in the host. The clone that showed the target enzyme's highest activity is said to respond specifically to growth inhibitors, whereby both quercetin and F1 were proven to be potential growth inhibitors as assessed by the MTT assay. In the process, quercetin reduced cell proliferation by inducing apoptosis and cell cycle arrest (S phase only), whereas F1 reduced cell proliferation by inducing cell cycle arrest only (S and G2 phases). Quercetin and F1 induced CYP1A1 and CYP1B1 (carcinogenicity) gene mRNA expression, but only F1 induced CYP2S1 (cytotoxicity) gene mRNA expression in the treated cells, suggesting that both quercetin and F1 inhibited the cell proliferation of MDA-MB-231 via different manners. The newly developed GS115-pPIC3.5K-hTopI can be used to select various potential substances for breast cancer treatment in the future.