scholarly journals Human SP-A1 (SFTPA1) variant-specific 3′ UTRs and poly(A) tail differentially affect the in vitro translation of a reporter gene

2010 ◽  
Vol 299 (4) ◽  
pp. L523-L534 ◽  
Author(s):  
Patricia Silveyra ◽  
Guirong Wang ◽  
Joanna Floros

Human surfactant protein A (SP-A) is encoded by two functional genes (SFTPA1, SFTPA 2) with a high degree of sequence identity. Sequence differences among these genes and their genetic variants have been observed at the 5′ and 3′ untranslated regions (UTRs). In this work, we studied the impact on translation of the SFTPA1 (hSP-A1) and SFTPA2 (hSP-A2) gene 5′ UTR splice variants and 3′ UTR sequence variants, in the presence or absence of poly(A) tail. We generated constructs containing the luciferase reporter gene flanked upstream by one of the hSP-A 5′ UTR splice variants and/or downstream by one hSP-A 3′ UTR sequence variant. mRNA transcripts were prepared by in vitro transcription and used for either in vitro translation with a rabbit reticulocyte lysate or transient transfection of the lung adenocarcinoma cell line NCI-H441. The luciferase activity results indicate that hSP-A 5′ UTR and 3′ UTR together have an additive effect on translation. In this context, the hSP-A1 6A3 and 6A4 3′ UTR variants exhibited higher translation efficiency than the 6A2 variant ( P <0.05), whereas no significant difference was observed between the two hSP-A2 3′ UTRs studied (1A0, 1A3). Further sequence analysis revealed that a deletion of an 11-nucleotide (nt) element in both the 6A3 and 6A4 3′ UTR variants changes the predicted secondary structure stability and the number of putative miRNA binding sites. Removal of this 11-nt element in the 6A2 3′ UTR resulted in increased translation, and the opposite effect was observed when the 11-nt element was cloned in a guest 3′ UTR (6A3, 6A4). These results indicate that sequence differences among hSP-A gene variants may account for differential regulation at the translational level.

2015 ◽  
Vol 308 (1) ◽  
pp. L58-L75 ◽  
Author(s):  
Nikolaos Tsotakos ◽  
Patricia Silveyra ◽  
Zhenwu Lin ◽  
Neal Thomas ◽  
Mudit Vaid ◽  
...  

Surfactant protein A (SP-A), a molecule with roles in lung innate immunity and surfactant-related functions, is encoded by two genes in humans: SFTPA1 (SP-A1) and SFTPA2 (SP-A2). The mRNAs from these genes differ in their 5′-untranslated regions (5′-UTR) due to differential splicing. The 5′-UTR variant ACD′ is exclusively found in transcripts of SP-A1, but not in those of SP-A2. Its unique exon C contains two upstream AUG codons (uAUGs) that may affect SP-A1 translation efficiency. The first uAUG (u1) is in frame with the primary start codon (p), but the second one (u2) is not. The purpose of this study was to assess the impact of uAUGs on SP-A1 expression. We employed RT-qPCR to determine the presence of exon C-containing SP-A1 transcripts in human RNA samples. We also used in vitro techniques including mutagenesis, reporter assays, and toeprinting analysis, as well as in silico analyses to determine the role of uAUGs. Exon C-containing mRNA is present in most human lung tissue samples and its expression can, under certain conditions, be regulated by factors such as dexamethasone or endotoxin. Mutating uAUGs resulted in increased luciferase activity. The mature protein size was not affected by the uAUGs, as shown by a combination of toeprint and in silico analysis for Kozak sequence, secondary structure, and signal peptide and in vitro translation in the presence of microsomes. In conclusion, alternative splicing may introduce uAUGs in SP-A1 transcripts, which in turn negatively affect SP-A1 translation, possibly affecting SP-A1/SP-A2 ratio, with potential for clinical implication.


2011 ◽  
Vol 301 (5) ◽  
pp. L795-L803 ◽  
Author(s):  
Patricia Silveyra ◽  
Manmeet Raval ◽  
Brett Simmons ◽  
Susan DiAngelo ◽  
Guirong Wang ◽  
...  

Two human genes, SFTPA1 (SP-A1) and SFTPA2 (SP-A2), encode surfactant protein A, a molecule of innate immunity and surfactant-related functions. Several genetic variants have been identified for both genes. These include nucleotide (nt) polymorphisms, as well as alternative splicing patterns at the 5′ untranslated region (5′UTR). Exon B (eB) is included in the 5′UTR of most SP-A2, but not SP-A1 splice variants. We investigated the role of eB in the regulation of gene expression and translation efficiency. A luciferase (Luc) reporter gene was cloned downstream of the entire (AeBD) or eB deletion mutants (del_mut) of the SP-A2 5′UTR, or heterologous 5′UTRs containing the eB sequence, or a random sequence of equal length. The del_mut constructs consisted in consecutive deletions of five nucleotides ( n = 8) within eB and the exon-exon junctions in the AeBD 5′UTR. Luc activities and mRNA levels were compared after transfection of NCI-H441 cells. We found that 1) eB increased Luc mRNA levels when placed upstream of heterologous 5′UTR sequences or the promoter region, regardless of its position and orientation; 2) translation efficiency of in vitro-generated mRNAs containing eB was higher than that of mRNAs without eB; and 3) the integrity of eB sequence is crucial for transcription and translation of the reporter gene. Thus eB 1) is a transcription enhancer, because it increases mRNA content regardless of position and orientation, 2) enhances translation when placed in either orientation within its natural 5′UTR sequence and in heterologous 5′UTRs, and 3) contains potential regulatory elements for both transcription and translation. We conclude that eB sequence and length are determinants of transcription and translation efficiency.


Tumor Biology ◽  
2021 ◽  
Vol 43 (1) ◽  
pp. 11-26
Author(s):  
Maike Busch ◽  
Natalia Miroschnikov ◽  
Jaroslaw Thomas Dankert ◽  
Marc Wiesehöfer ◽  
Klaus Metz ◽  
...  

BACKGROUND: Retinoblastoma (RB) is the most common childhood eye cancer. Chemotherapeutic drugs such as etoposide used in RB treatment often cause massive side effects and acquired drug resistances. Dysregulated genes and miRNAs have a large impact on cancer progression and development of chemotherapy resistances. OBJECTIVE: This study was designed to investigate the involvement of retinoic acid receptor alpha (RARα) in RB progression and chemoresistance as well as the impact of miR-138, a potential RARα regulating miRNA. METHODS: RARα and miR-138 expression in etoposide resistant RB cell lines and chemotherapy treated patient tumors compared to non-treated tumors was revealed by Real-Time PCR. Overexpression approaches were performed to analyze the effects of RARα on RB cell viability, apoptosis, proliferation and tumorigenesis. Besides, we addressed the effect of miR-138 overexpression on RB cell chemotherapy resistance. RESULTS: A binding between miR-138 and RARα was shown by dual luciferase reporter gene assay. The study presented revealed that RARα is downregulated in etoposide resistant RB cells, while miR-138 is endogenously upregulated. Opposing RARα and miR-138 expression levels were detectable in chemotherapy pre-treated compared to non-treated RB tumor specimen. Overexpression of RARα increases apoptosis levels and reduces tumor cell growth of aggressive etoposide resistant RB cells in vitro and in vivo. Overexpression of miR-138 in chemo-sensitive RB cell lines partly enhances cell viability after etoposide treatment. CONCLUSIONS: Our findings show that RARα acts as a tumor suppressor in retinoblastoma and is downregulated upon etoposide resistance in RB cells. Thus, RARα may contribute to the development and progression of RB chemo-resistance.


Author(s):  
Mattapudi Basavaiah Babu ◽  
T. B. V. G. Raju ◽  
N. Mahendra Varma ◽  
Gowtam Dev Dondapati ◽  
Srivalli Podili ◽  
...  

Aim: To evaluate the impact of environmental pH on intra-radicular dentin push-out bond strengths of MTA, MTA HP, and Biodentine. Materials and Methodology: Freshly extracted human mandibular single-rooted premolars or maxillary anterior incisors that were either intact or contained only small carious lesions were selected.120 mid root dentins is horizontally divided into 1.0 mm thick slices and divided into 3 MTA, MTA HP, BIODENTINE groups. The compressive load is applied at a speed of 0.5 mm/min by exerting a downward pressure on the outer surface of MTA using a 1.00 mm diameter cylindrical stainless-steel plunger. Maximum load to MTA was reported in newtons at the time of dislodgement and converted to megapascals. The 1-way analysis of variance test was used to compare the push-out bond strength of the groups with the same storage time (4 or 34 days), followed by the pair-wise comparison of the Tukey post hoc test. The Student's t-test was used to evaluate 3-group means. At P = .005, the degree of significance was set. Thus the clinical importance of the present study states that considering several factors like microhardness, composition by products, particle sizes and the environmental pH plays a critical role in selection of root end filling material. Results: There was significant difference between groups (P = .001) after 4 days of PBS and Acid condition, where Bio dentine had significantly the highest bond strength. Conclusion: The strength of MTA HP, BIODENTINE, MTA materials at dentine interface increases over 30 days in the storage of PBS solution at pH 7.4, after an initial acid challenge by acetic acid of pH 5.4, which decreases initial bond strength.


2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Stef De Lombaerde ◽  
Ken Kersemans ◽  
Sara Neyt ◽  
Jeroen Verhoeven ◽  
Christian Vanhove ◽  
...  

Introduction. An in vivo determination of bile acid hepatobiliary transport efficiency can be of use in liver disease and preclinical drug development. Given the increased interest in bile acid Positron Emission Tomography- (PET-) imaging, a further understanding of the impact of 18-fluorine substitution on bile acid handling in vitro and in vivo can be of significance. Methods. A number of bile acid analogues were conceived for nucleophilic substitution with [18F]fluoride: cholic acid analogues of which the 3-, 7-, or 12-OH function is substituted with a fluorine atom (3α-[18F]FCA; 7β-[18F]FCA; 12β-[18F]FCA); a glycocholic and chenodeoxycholic acid analogue, substituted on the 3-position (3β-[18F]FGCA and 3β-[18F]FCDCA, resp.). Uptake by the bile acid transporters NTCP and OATP1B1 was evaluated with competition assays in transfected CHO and HEK cell lines and efflux by BSEP in membrane vesicles. PET-scans with the tracers were performed in wild-type mice (n=3 per group): hepatobiliary transport was monitored and compared to a reference tracer, namely, 3β-[18F]FCA. Results. Compounds 3α-[18F]FCA, 3β-[18F]FGCA, and 3β-[18F]FCDCA were synthesized in moderate radiochemical yields (4–10% n.d.c.) and high radiochemical purity (>99%); 7β-[18F]FCA and 12β-[18F]FCA could not be synthesized and included further in this study. In vitro evaluation showed that 3α-FCA, 3β-FGCA, and 3β-FCDCA all had a low micromolar Ki-value for NTCP, OATP1B1, and BSEP. In vivo, 3α-[18F]FCA, 3β-[18F]FGCA, and 3β-[18F]FCDCA displayed hepatobiliary transport with varying efficiency. A slight yet significant difference in uptake and efflux rate was noticed between the 3α-[18F]FCA and 3β-[18F]FCA epimers. Conjugation of 3β-[18F]FCA with glycine had no significant effect in vivo. Compound 3β-[18F]FCDCA showed a significantly slower hepatic uptake and efflux towards gallbladder and intestines. Conclusion. A set of 18F labeled bile acids was synthesized that are substrates of the bile acid transporters in vitro and in vivo and can serve as PET-biomarkers for hepatobiliary transport of bile acids.


1998 ◽  
Vol 18 (2) ◽  
pp. 978-988 ◽  
Author(s):  
Brian K. Meyer ◽  
Marilyn G. Pray-Grant ◽  
John P. Vanden Heuvel ◽  
Gary H. Perdew

ABSTRACT Prior to ligand activation, the unactivated aryl hydrocarbon receptor (AhR) exists in a heterotetrameric 9S core complex consisting of the AhR ligand-binding subunit, a dimer of hsp90, and an unknown subunit. Here we report the purification of an ∼38-kDa protein (p38) from COS-1 cell cytosol that is a member of this complex by coprecipitation with a FLAG-tagged AhR. Internal amino acid sequence information was obtained, and p38 was identified as the hepatitis B virus X-associated protein 2 (XAP2). The simian ortholog of XAP2 was cloned from a COS-1 cDNA library; it codes for a 330-amino-acid protein containing regions of homology to the immunophilins FKBP12 and FKBP52. A tetratricopeptide repeat (TPR) domain in the carboxy-terminal region of XAP2 was similar to the third and fourth TPR domains of human FKBP52 and the Saccharomyces cerevisiae transcriptional modulator SSN6, respectively. Polyclonal antibodies raised against XAP2 recognized p38 in the unliganded AhR complex in COS-1 and Hepa 1c1c7 cells. It was ubiquitously expressed in murine tissues at the protein and mRNA levels. It was not required for the assembly of an AhR-hsp90 complex in vitro. Additionally, XAP2 did not directly associate with hsp90 upon in vitro translation, but was present in a 9S form when cotranslated in vitro with murine AhR. XAP2 enhanced the ability of endogenous murine and human AhR complexes to activate a dioxin-responsive element–luciferase reporter twofold, following transient expression of XAP2 in Hepa 1c1c7 and HeLa cells.


Folia Medica ◽  
2017 ◽  
Vol 59 (1) ◽  
pp. 23-30 ◽  
Author(s):  
Kalpesh C. Ashara ◽  
Ketan V. Shah

Abstract Background: Ophthalmic formulations of chloramphenicol have poor bioavailability of chloramphenicol in the ocular cavity. Aim: The present study aimed at exploring the impact of different oil mixtures in the form of emulsion on the permeability of chloramphenicol after ocular application. Materials and methods: Selection of oil mixture and ratio of the components was made by an equilibrium solubility method. An emulsifier was chosen according to its emulsification properties. A constrained simplex centroid design was used for the assessment of the emulsion development. Emulsions were evaluated for physicochemical properties; zone of inhibition, in-vitro diffusion and ex-vivo local accumulation of chloramphenicol. Validation of the design using check-point batch and reduced polynomial equations were also developed. Optimization of the emulsion was developed by software Design® expert 6.0.8. Assessment of the osmolarity, ocular irritation, sterility testing and isotonicity of optimized batch were also made. Results: Parker Neem®, olive and peppermint oils were selected as an oil phase in the ratio 63.64:20.2:16.16. PEG-400 was selected as an emulsifier according to a pseudo-ternary phase diagram. Constrained simplex-centroid design was applied in the range of 25-39% water, 55-69% PEG-400, 5-19% optimized oil mixture, and 1% chloramphenicol. Unpaired Student’s t-test showed for in-vitro and ex-vivo studies that there was a significant difference between the optimized batch of emulsion and Chloramphenicol eye caps (a commercial product) according to both were equally safe. Conclusion: The optimized batch of an emulsion of chloramphenicol was found to be as safe as and more effective than Chloramphenicol eye caps.


2014 ◽  
Vol 2014 ◽  
pp. 1-11
Author(s):  
Ya-Ju Hsieh ◽  
Luen Hwu ◽  
Chien-Chih Ke ◽  
Skye Hsin-Hsien Yeh ◽  
Chien-Feng Lin ◽  
...  

Multimodality imaging using noncytotoxic triple fusion (TF) reporter genes is an important application for cell-based tracking, drug screening, and therapy. The firefly luciferase(fl), monomeric red fluorescence protein(mrfp), and truncated herpes simplex virus type 1 thymidine kinase SR39 mutant(ttksr39)were fused together to create TF reporter gene constructs with different order. The enzymatic activities of TF protein in vitro andin vivowere determined by luciferase reporter assay,H-FEAU cellular uptake experiment, bioluminescence imaging, and micropositron emission tomography (microPET). The TF construct expressed in H1299 cells possesses luciferase activity and red fluorescence. The tTKSR39 activity is preserved in TF protein and mediates high levels ofH-FEAU accumulation and significant cell death from ganciclovir (GCV) prodrug activation. In living animals, the luciferase and tTKSR39 activities of TF protein have also been successfully validated by multimodality imaging systems. The red fluorescence signal is relatively weak forin vivoimaging but may expedite FACS-based selection of TF reporter expressing cells. We have developed an optimized triple fusion reporter constructDsRedm-fl-ttksr39for more effective and sensitivein vivoanimal imaging using fluorescence, bioluminescence, and PET imaging modalities, which may facilitate different fields of biomedical research and applications.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1520-1520
Author(s):  
Anja Troeger ◽  
Gabriele Escherich ◽  
Udo zur Stadt ◽  
M. L Den Boer ◽  
Rob Pieters ◽  
...  

Abstract Early identification of patients (pts) at risk for relapse allows for development of risk-adapted treatment strategies, thus steadily improving the outcome in pediatric acute lymphoblastic leukemia (ALL). Besides classic prognostic factors such as age, initial leukocyte count (WBC), genetic alterations and the immune phenotype, the so called PVA Score, summarizing the in vitro resistance of blasts against prednisone, vincristine and asparaginase, has been applied for treatment stratification in the CoALL protocol, a German multicenter study for children with ALL. Over the past years it has become increasingly clear that the in vivo response to chemotherapy assessed by detection of residual malignant cells (MRD) by PCR technique can be predictive of prognosis. Here we compare for the first time the relevance of in vitro (PVA Score) and in vivo (MRD) treatment response in a large cohort of 275 children with ALL, age 1–17 years, uniformly treated according to the CoALL protocols 05–92 to 07–03. Children with B cell precursor ALL (BCP-ALL) and T-ALL were analyzed separately. Bone marrow samples of 160 children with BCP-ALL and of 115 T-ALL pts diagnosed between 1992–2005 were prospectively assessed for PVA Score at diagnosis and MRD levels at day (d) 15, 29 and 43 after informed consent was obtained from the parents or legal guardians at the time of enrolment. Of note, 7 of the BCP-ALL and 14 of the T-ALL pts with late morphological response were excluded from analysis. Overall median MRD levels in BCP-ALL pts (MRDd15: 6×10e-4; MRDd29: 2×10e-5) were one log lower than in T-ALL (MRDd15: 9×10e-3; MRDd29: 3×10e-4). We detected no association between PVA Score and MRD level in BCP-ALL (correlation coefficient: r=0.15; p=0.15) and only a weak correlation in T-ALL pts (correlation coefficient: r=0.43; p=0.0003). When assessing the impact of the PVA Score on relapse free survival (RFS), in BCP-ALL only score 3+4 (good response) vs. 8+9 (poor response) was prognostically relevant (RFS 0.86±0.05 vs. 0.59±0.12; p=0.03), whereas in T-ALL no significant difference between these subgroups was found (RFS 0.71±0.1 vs. 0.68±0.1; p=0.62). In multivariate analysis PVA Score 3+4 vs. 8+9 remained the most relevant parameter for RFS in BCP-ALL (p=0.05) when compared to age and initial WBC. However, MRD levels were of even higher predictive power, especially at later time points: MRD negativity at d29 in BCP-ALL identified pts with significantly superior RFS (RFS MRD neg.: 0.9±0.05 vs. pos.: 0.7±0.05; p=0.003) and low MRD levels indicated a favorable outcome in T-ALL (RFS MRD &lt;10e-3: 0.89±0.05 vs. MRD &gt;10e-3: 0.68±0.07; p=0.001). Moreover, both BCP-ALL and T-ALL pts characterized by MRD levels &gt;10e-3 on d43 exhibited a poor outcome (RFS BCP-ALL: 0.42±0.17; RFS T-ALL: 0.47±0.14). MRD remained an independent marker in multivariate analysis including initial WBC and age, both in BCP- (MRDd29: p=0.006; MRDd43: p=0.001) and T-ALL (MRDd29: p=0.003; MRDd43: p=0.015). By multivariate analysis, in T-ALL low MRD levels on d29 predicted superior RFS independently from the PVA Score (MRD: p=0.002 vs. PVA: p=0.09), whereas in BPC-ALL these parameters were not completely independent from each other at that early time point (MRD: p= 0.059 vs. PVA: p= 0.063) but became independent at d43 (MRD: p= 0.018 vs. PVA: p= 0.253). While the predictive value of the PVA Score was limited to BCP-ALL, MRD was an independent prognostic marker for both BCP- and T-ALL and reliably identified pts at low and high risk for relapse.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 541-541
Author(s):  
Yesim Dargaud ◽  
Maureane Hoffman ◽  
Claude Negrier ◽  
Leana Lefrapper ◽  
Dougald M. Monroe

Abstract Abstract 541 Bleeding occurs in from 10 – 16% of warfarin-treated patients. Having a PT-INR in the target range is associated with better outcomes. However, even patients with an INR in the target range of 2–3 can suffer bleeding, suggesting that INR does not perfectly reflect the therapeutic effect of warfarin. The goal of our studies was to determine whether the level of specific coagulation factors could predict the risk of bleeding while the INR was in the target range. We modeled warfarin anticoagulation in our previously published in vitro cell based-model by adjusting the levels of vitamin K-dependent factors to those of patients with an INR of 2–3. We then examined the effect of variations in the level of FIX. The cogulation reactions were initiated by monocyte-expressed tissue factor (assayed at 1pM). Variation in FIX had a marked effect on thrombin generation. However, in plasma with the same levels of factors, as expected, variations in FIX had no effect on the PT-INR. Thus, we hypothesized that a subject with a lower FIX level than average may have a lower level of thrombin generation than is indicated by the INR. The INR might, therefore, underestimate the level of anticoagulation in such a subject. If s/he is maintained in the “therapeutic range” as measured by the INR, s/he will actually be over-anticoagulated and prone to hemorrhage. A prospective, single centre clinical study has been carried out to test this hypothesis in warfarinized patients. Between October 2010 and June 2011, 312 consecutive patients admitted to the emergency department of Edouard Herriot Hospital in Lyon, with an INR between 1.8 and 3.2, were included in the study after obtaining informed consent. Twenty six patients were admitted for a bleeding episode, 18 for recurrent thrombosis and 268 for other medical reasons. Patients presenting with bleeding, 17 males and 9 females, were aged 74±14 years old compared to the rest of the patients aged 76±14. Among the 26 bleeders, 7 had a spontaneous intracranial haemorrhage, 2 had a trauma-induced intracranial haemorrhage, 12 presented a gastrointestinal bleeding and 5 exhibited muscle hematomas, severe epistaxis or urinary tract bleeding. PT-INR and vitamin K-dependent factor levels were determined in all patients. Thrombin generation capacity in platelet poor plasma was measured using Calibrated Automated Thrombin generation assay (Thrombinoscope bv, Maastricht, The Netherlands), with tissue factor 1pM and phospholipids PC:PS:PE 4μM. No statistically significant difference was observed in the PT-INR of bleeding patients (INR=2.4±0.4) and those having a thrombosis (INR=2.5±0.5) or patients admitted for other reasons (INR=2.6±0.2). Plasma prothrombin and factor × levels were also similar in all three groups. However, a statistically lower plasma factor IX activity was observed in bleeders (p=0.01, Mann Whitney test) compared to other groups, 47.6±20 IU/dL vs. 63±33 IU/dL. In all the warfarinized subjects with an INR between 1.8 and 3.2, no correlation was found between thrombin generation capacity and PT-INR results (p=0.85, Spearman correlation test). However, a statistically significant correlation was observed between thrombin generation capacity and factor IX levels (p=0.0002). In patients, presenting with warfarin-related haemorrhage, the endogenous thrombin potential (ETP) was significantly lower at 340±335 nM.min (p=0.05) then that of warfarinized subjects who did not suffer bleeding (ETP 406±215 nM.min). These data support our hypothesis based on our in vitro results and show that patients who bleed when their PT-INR is in the target range 2 – 3 might have defective thrombin generation related to a lower level of factor IX than expected. Thus, our results suggest that the appropriate target INR level might not be the same for all patients. Those with factor IX levels that differ significantly from the mean of the population might be managed best by selecting a target INR that is based on the level of thrombin generation. Of course, a “target range” for parameters of thrombin generation during warfarin therapy would need to be developed if the assay were to be used for this purpose. Disclosures: No relevant conflicts of interest to declare.


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