qPCR Master Mix Research Articles

TGFb signature at 2 weeks to predict response to preoperative therapy (PT) with bevacizumab (B) and chemotherapy (CT) in early breast cancer (EBC).

1046 Background: Gene expression profiles from core biopsies taken during PT for EBC may identify markers associated with benefit. B was recently shown to improve pathologic complete response (pCR) to CT in two randomized trials, but is associated with increased toxicity. Predictive signatures are critical to optimizing benefit. We have shown that changes in TGF-β pathway activity after one dose of B are associated with pCR. To confirm these results and understand the mechanism of alteration of the TGFb pathway, we evaluated the 61-gene TGFb signature by RT-PCR, measured markers of TGFb pathway activation and assessed TGFb gene mutations. Methods: Real-time PCR was performed on paired (pre/post) core biopsy RNA samples from 21 patients (pts) who received B, trastuzumab (T) or nab-paclitaxel prior to combined CT and targeted therapy using Custom RT2 Profiler PCR Arrays (384-well plate, 64x6 format) containing 60 genes from our TGF-beta signature and 3 housekeeping genes, IPO8, ALAS1, and SDHA. RT- PCR reactions containing Qiagen RT2SYBR Green qPCR Mastermix and 5 ng of amplified cDNA were run on a Roche LightCycler480 machine. Cp values were determined using the Roche LightCycler480 software. Antibodies to p-Smad2, TGFBR1 and TGFBR2 were analyzed in FFPE IHC pre and post therapy. TGFb pathway genes with known mutations in TCGA were assessed using an Illumina Custom Amplicon and miSeq next generation sequencing. Results: The log 2 FPKM value of the 60 genes correlated well with the ΔCP values calculated normalized to ALAS1 housekeeping gene. The ΔΔCP values was determined by subtracting the 60 gene ΔCP values of baseline samples from post-exposure samples. Patients were clustered using the ΔΔCP. Pts exposed to B who achieved a pCR showed down-regulation of signatures genes, in contrast to a strong non-pCR cluster. Signature evaluation showed no association with response in the T arm. TGFb pathway protein expression and mutation frequency is under analysis. Conclusions: TGFb signature predicts response to B containing chemotherapy after one dose of B and is validated by RT- PCR as a potential predictive tool. TGFb pathway activation and gene mutation analysis will be presented. Clinical trial information: NCT00617942.

Spdef Null Mice Lack Conjunctival Goblet Cells and Provide a Model of Dry Eye

Goblet cell numbers decrease within the conjunctival epithelium in drying and cicatrizing ocular surface diseases. Factors regulating goblet cell differentiation in conjunctival epithelium are unknown. Recent data indicate that the transcription factor SAM-pointed domain epithelial-specific transcription factor (Spdef) is essential for goblet cell differentiation in tracheobronchial and gastrointestinal epithelium of mice. Using Spdef(-/-) mice, we determined that Spdef is required for conjunctival goblet cell differentiation and that Spdef(-/-) mice, which lack conjunctival goblet cells, have significantly increased corneal surface fluorescein staining and tear volume, a phenotype consistent with dry eye. Microarray analysis of conjunctival epithelium in Spdef(-/-) mice revealed down-regulation of goblet cell-specific genes (Muc5ac, Tff1, Gcnt3). Up-regulated genes included epithelial cell differentiation/keratinization genes (Sprr2h, Tgm1) and proinflammatory genes (Il1-α, Il-1β, Tnf-α), all of which are up-regulated in dry eye. Interestingly, four Wnt pathway genes were down-regulated. SPDEF expression was significantly decreased in the conjunctival epithelium of Sjögren syndrome patients with dry eye and decreased goblet cell mucin expression. These data demonstrate that Spdef is required for conjunctival goblet cell differentiation and down-regulation of SPDEF may play a role in human dry eye with goblet cell loss. Spdef(-/-) mice have an ocular surface phenotype similar to that in moderate dry eye, providing a new, more convenient model for the disease.

Type VIII Collagen Mediates Vessel Wall Remodeling after Arterial Injury and Fibrous Cap Formation in Atherosclerosis

Collagens in the atherosclerotic plaque signal regulation of cell behavior and provide tensile strength to the fibrous cap. Type VIII collagen, a short-chain collagen, is up-regulated in atherosclerosis; however, little is known about its functions invivo. We studied the response to arterial injury and the development of atherosclerosis in type VIII collagen knockout mice (Col8(-/-) mice). After wire injury of the femoral artery, Col8(-/-) mice had decreased vessel wall thickening and outward remodeling when compared with Col8(+/+) mice. We discovered that apolipoprotein E (ApoE) is an endogenous repressor of the Col8a1 chain, and, therefore, in ApoE knockout mice, type VIII collagen was up-regulated. Deficiency of type VIII collagen in ApoE(-/-) mice (Col8(-/-);ApoE(-/-)) resulted in development of plaques with thin fibrous caps because of decreased smooth muscle cell migration and proliferation and reduced accumulation of fibrillar type I collagen. In contrast, macrophage accumulation was not affected, and the plaques had large lipid-rich necrotic cores. We conclude that in atherosclerosis, type VIII collagen is up-regulated in the absence of ApoE and functions to increase smooth muscle cell proliferation and migration. This is an important mechanism for formation of a thick fibrous cap to protect the atherosclerotic plaque from rupture.

Evaluation of five DNA extraction systems for recovery of DNA from bone

Five DNA extraction systems were assessed for their DNA extraction efficiency on samples of fresh pig bone. Four commercially available silica-based extraction kits (ChargeSwitch® gDNA Plant Kit (Life Technologies), DNA IQTM System Kit (Promega), DNeasy® Blood & Tissue Kit (Qiagen) and PrepFiler® BTA Forensic DNA Extraction Kit (Life Technologies)) and a conventional phenol-chloroform method were tested in this study. Extracted DNA samples were quantitated with GoTaq® qPCR Master Mix (Promega) using an Applied Biosystems® 7500 Real-Time PCR System and the extracts were amplified using an in-house multiplex system. The phenol-chloroform extraction produced higher yields of DNA than the silica-based extraction methods. Among the silica-based extractions ChargeSwitch® gDNA Plant Kit recovered the highest amounts of DNA. However, all methods produced DNA that could be amplified and none of the extracts contained any detectable inhibition.

Ras-induced Up-regulation of CTP:Phosphocholine Cytidylyltransferase α Contributes to Malignant Transformation of Intestinal Epithelial Cells

Cancer cells have enhanced lipogenic capacity characterized by increased synthesis of fatty acids and complex lipids, including phosphatidylcholine (PC). As the rate-limiting enzyme in the CDP-choline pathway for PC synthesis, CTP:phosphocholine cytidylyltransferase α (CCTα) is implicated in the provision of membranes and bioactive lipids necessary of cell proliferation. In this study, we assessed the role of CCTα in malignant intestinal epithelial cells transformed with activated H-ras (IEC-ras). Three IEC-ras clones had significant up-regulation CCTα expression, but PC synthesis and in vitro activity of CCTα were similar to control IEC. RNA interference of CCTα in adherent IEC-ras did not affect PC synthesis, confirming that the enzyme was relatively inactive. However, CCTα silencing in ras-transformed IEC reduced anchorage-independent growth, a criterion for malignant transformation, as well as tumorigenicity in mice. Relative to their adherent counterparts, detached IEC-ras had increased PC synthesis that was attenuated by inducible CCTα silencing. Detachment of IEC-ras was accompanied by increased CCTα phosphorylation and cytosolic enzyme activity. We conclude that the expanded pool of CCTα in IEC-ras is activated by detachment. This provides the increased PC biosynthetic capacity that contributes to malignant transformation of intestinal epithelial cells when detached from the extracellular matrix.

208 COMPARISON OF THE EXPRESSION OF SOX2 AND Stat3 IN BOVINE BLASTOCYST AND HATCHED BLASTOCYST

The investigation of the transcription factors involved in the regulation of pluripotency in pre-implantation embryos of cattle provides important information regarding the early embryonic development and derivation of embryonic stem cells. The present experiment aimed to compare the level of expression of SOX 2 and Stat3, pluripotency markers, in bovine blastocysts (D7) and hatched blastocysts (D10), because it is known that around hatching, the inner cell mass (ICM) differentiates into hypoblast and epiblast. Cumulus–oocyte complexes were matured in TCM 199 for 24 h and fertilized with frozen–thawed sperm. Presumptive zygotes were cultured in SOFaaci for 7 days (group 1) and for 10 days (group 2). All embryos were washed 3 times in PBS, pooled, and frozen at –80°C until RNA extraction. For quantification of SOX2 and Stat3 mRNA levels, total RNA was isolated from pools of 7 embryos per replicate (n = 3) and for each examined developmental stage using RNeasy Micro Kit (Qiagen). The reverse transcriptase Superscript III (Invitrogen) was used for the synthesis of cDNA (cDNA), and the qPCR was performed with the Gotaq qPCR Master Mix (Promega, Madison, WI, USA). As negative control, cDNA was replaced by nuclease-free water in the qPCR reaction. Quantification of expression was determined by the relative standard curve method and normalized to the housekeeping gene YWHAZ. Standard curves for SOX2, Stat 3, and YWHAZ were derived from 10-fold serial dilutions of bovine DNA and gave correlation coefficients greater than 0.99 and efficiencies greater than 94%. The data from 3 replicates were analysed by ANOVA, and it was found that the level of SOX2 abundance is 9.8-fold higher in D7 blastocyst cells compared with D10 blastocyst cells, and the level of Stat 3 transcription is 1.5-fold higher in blastocyst cells than in hatched blastocysts. The expression of pluripotency markers SOX2 and Stat3 was significantly higher in embryos with 7 days of development because at this stage the MCI had not yet begun the process of differentiation. Support of FAPESP is acknowledged.

Multi-platform comparison of ten commercial master mixes for probe-based real-time polymerase chain reaction detection of bioterrorism threat agents for surge preparedness

The Centers for Disease Control and Prevention and United States Army Research Institute for Infectious Diseases have developed real-time PCR assays for the detection of bioterrorism threat agents. These assays all rely on a limited number of approved real-time PCR master mixes. Because the availability of these reagents is a critical element of bioterrorism preparedness, we undertook a joint national preparedness exercise to address the potential surge needs resulting from a large-scale bio-emergency. We identified 9 commercially-available potential alternatives to an existing approved master mix (LightCycler FastStart DNA Master HybProbes): the TaqMan Fast Universal PCR master mix, OmniMix HS, FAST qPCR master mix, EXPRESS qPCR SuperMix kit, QuantiFast Probe PCR kit, LightCycler FastStart DNA MasterPLUS HybProbe, Brilliant II FAST qPCR master mix, ABsolute Fast QPCR Mix and the HotStart IT Taq master mix. The performances of these kits were evaluated by the use of real-time PCR assays for four bioterrorism threat agents: Bacillus anthracis, Brucella melitensis, Burkholderia mallei and Francisella tularensis. The master mixes were compared for target-specific detection levels, as well as consistency of results among three different real-time PCR platforms (LightCycler, SmartCycler and 7500 Fast Dx). Real-time PCR analysis revealed that all ten kits performed well for agent detection on the 7500 Fast Dx instrument; however, the QuantiFast Probe PCR kit yielded the most consistently positive results across multiple real-time PCR platforms. We report that certain combinations of commonly used master mixes and instruments are not as reliable as others at detecting low concentrations of target DNA. Furthermore, our study provides laboratories the option to select from the commercial kits we evaluated to suit their preparedness needs.

Optimizing a qPCR Gene Expression Quantification Assay for S. epidermidis Biofilms: A Comparison between Commercial Kits and a Customized Protocol

Staphylococcus epidermidis biofilm-related infections are a current concern within the medical community due to their high incidence and prevalence, particularly in patients with indwelling medical devices. Biofilm gene expression analysis by quantitative real-time PCR (qPCR) has been increasingly used to understand the role of biofilm formation in the pathogenesis of S. epidermidis infections. However, depending on the RNA extraction procedure, and cDNA synthesis and qPCR master mixes used, gene expression quantification can be suboptimal. We recently showed that some RNA extraction kits are not suitable for S. epidermidis biofilms, due to sample composition, in particular the presence of the extracellular matrix. In this work, we describe a custom RNA extraction assay followed by the evaluation of gene expression using different commercial reverse transcriptase kits and qPCR master mixes. Our custom RNA extraction assay was able to produce good quality RNA with reproducible gene expression quantification, reducing the time and the costs associated. We also tested the effect of reducing cDNA and qPCR reaction volumes and, in most of the cases tested, no significant differences were found. Finally, we titered the SYBR Green I concentrations in standard PCR master mixes and compared the normalized expression of the genes icaA, bhp, aap, psmβ1 and agrB using 4 distinct biofilm forming S. epidermidis strains to the results obtained with commercially available kits. The overall results demonstrated that despite some statistically, but not biologically significant differences observed, the customized qPCR protocol resulted in the same gene expression trend presented by the commercially available kits used.

Roles for Peroxisome Proliferator-activated Receptor γ (PPARγ) and PPARγ Coactivators 1α and 1β in Regulating Response of White and Brown Adipocytes to Hypoxia

Obese white adipose tissue is hypoxic but is incapable of inducing compensatory angiogenesis. Brown adipose tissue is highly vascularized, facilitating delivery of nutrients to brown adipocytes for heat production. In this study, we investigated the mechanisms by which white and brown adipocytes respond to hypoxia. Brown adipocytes produced lower amounts of hypoxia-inducible factor 1α (HIF-1α) than white adipocytes in response to low O(2) but induced higher levels of hypoxia-associated genes. The response of white adipocytes to hypoxia required HIF-1α, but its presence alone was incapable of inducing target gene expression under normoxic conditions. In addition to the HIF-1α targets, hypoxia also induced many inflammatory genes. Exposure of white adipocytes to a peroxisome proliferator-activated receptor γ (PPARγ) ligand (troglitazone) attenuated induction of these genes but enhanced expression of the HIF-1α targets. Knockdown of PPARγ in mature white adipocytes prevented the usual robust induction of HIF-1α targets in response to hypoxia. Similarly, knockdown of PPARγ coactivator (PGC) 1β in PGC-1α-deficient brown adipocytes eliminated their response to hypoxia. These data demonstrate that the response of white adipocytes requires HIF-1α but also depends on PPARγ in white cells and the PPARγ cofactors PGC-1α and PGC-1β in brown cells.

Deletion of the Scl +19 enhancer increases the blood stem cell compartment without affecting the formation of mature blood lineages

The stem cell leukemia (Scl)/Tal1 gene is essential for normal blood and endothelial development, and is expressed in hematopoietic stem cells (HSCs), progenitors, erythroid, megakaryocytic, and mast cells. The Scl +19 enhancer is active in HSCs and progenitor cells, megakaryocytes, and mast cells, but not mature erythroid cells. Here we demonstrate that in vivo deletion of the Scl +19 enhancer (SclΔ19/Δ19) results in viable mice with normal Scl expression in mature hematopoietic lineages. By contrast, Scl expression is reduced in the stem/progenitor compartment and flow cytometry analysis revealed that the HSC and megakaryocyte-erythroid progenitor populations are enlarged in SclΔ19/Δ19 mice. The increase in HSC numbers contributed to enhanced expansion in bone marrow transplantation assays, but did not affect multilineage repopulation or stress responses. These results affirm that the Scl +19 enhancer plays a key role in the development of hematopoietic stem/progenitor cells, but is not necessary for mature hematopoietic lineages. Moreover, active histone marks across the Scl locus were significantly reduced in SclΔ19/Δ19 fetal liver cells without major changes in steady-state messenger RNA levels, suggesting post-transcriptional compensation for loss of a regulatory element, a result that might be widely relevant given the frequent observation of mild phenotypes after deletion of regulatory elements.

Altered expression of microRNA miR-146a correlates with the development of chronic renal inflammation

MicroRNAs (miRNAs) are highly conserved small non-coding RNAs that act as post-transcriptional regulators of target mRNA. In this study, we sought to identify the microRNA underlying local inflammation in a murine model of chronic kidney disease (CKD). In microarray analysis of kidneys, the expression of miR-146a/b was elevated in B6.MRLc1 CKD mice that spontaneously develop renal inflammation with age. Primary-microRNA analysis found that elevated miR-146a/b expression in the kidneys of B6.MRLc1 mice was mainly derived from miR-146a rather than miR-146b, and this expression increased with the development of CKD. Histopathological scores for glomerular and interstitial lesions, mRNA expression of inflammatory mediators, and macrophage infiltration were significantly higher in B6.MRLc1 than C57BL/6 mice and were positively correlated with miR-146a expression. In situ hybridization and laser microdissection-RT-PCR showed that miR-146a expression in interstitial lesions containing inflammatory cells was higher than in the glomerulus. The increased expression of the inflammatory-associated genes RELA, IRAK1, IL1B, IL10, and CXCLs was noted in miR-146a/b-silenced human monocytes. The amount of miR-146a was higher in urine sediments of B6.MRLc1 than of C57BL/6 mice. Thus, miR-146a expression in the kidneys and its urinary excretion was specifically associated with the development of interstitial lesions and correlated with inflammatory cell infiltration.

Engineering Hyperthermophilic Archaeon Pyrococcus furiosus to Overproduce Its Cytoplasmic [NiFe]-Hydrogenase

The cytoplasmic hydrogenase (SHI) of the hyperthermophilic archaeon Pyrococcus furiosus is an NADP(H)-dependent heterotetrameric enzyme that contains a nickel-iron catalytic site, flavin, and six iron-sulfur clusters. It has potential utility in a range of bioenergy systems in vitro, but a major obstacle in its use is generating sufficient amounts. We have engineered P. furiosus to overproduce SHI utilizing a recently developed genetic system. In the overexpression (OE-SHI) strain, transcription of the four-gene SHI operon was under the control of a strong constitutive promoter, and a Strep-tag II was added to the N terminus of one subunit. OE-SHI and wild-type P. furiosus strains had similar rates of growth and H(2) production on maltose. Strain OE-SHI had a 20-fold higher transcription of the polycistronic hydrogenase mRNA encoding SHI, and the specific activity of the cytoplasmic hydrogenase was ∼10-fold higher when compared with the wild-type strain, although the expression levels of genes encoding processing and maturation of SHI were the same in both strains. Overexpressed SHI was purified by a single affinity chromatography step using the Strep-tag II, and it and the native form had comparable activities and physical properties. Based on protein yield per gram of cells (wet weight), the OE-SHI strain yields a 100-fold higher amount of hydrogenase when compared with the highest homologous [NiFe]-hydrogenase system previously reported (from Synechocystis). This new P. furiosus system will allow further engineering of SHI and provide hydrogenase for efficient in vitro biohydrogen production.

PTEN Regulates PDGF Ligand Switch for β-PDGFR Signaling in Prostate Cancer

Platelet-derived growth factor (PDGF) family members are potent growth factors that regulate cell proliferation, migration, and transformation. Clinical studies have shown that both PDGF receptor β (β-PDGFR) and its ligand PDGF D are up-regulated in primary prostate cancers and bone metastases, whereas PDGF B, a classic ligand for β-PDGFR, is not frequently detected in clinical samples. In this study, we examined the role of the tumor suppressor phosphatase and tensin homologue deleted on chromosome 10 (PTEN) in the regulation of PDGF expression levels using both a prostate-specific, conditional PTEN-knockout mouse model and mouse prostate epithelial cell lines established from these mice. We found an increase in PDGF D and β-PDGFR expression levels in PTEN-null tumor cells, accompanied by a decrease in PDGF B expression. Among Akt isoforms, increased Akt3 expression was most prominent in mouse PTEN-null cells, and phosphatidylinositol 3-kinase/Akt activity was essential for the maintenance of increased PDGF D and β-PDGFR expression. In vitro deletion of PTEN resulted in a PDGF ligand switch from PDGF B to PDGF D in normal mouse prostate epithelial cells, further demonstrating that PTEN regulates this ligand switch. Similar associations between PTEN status and PDGF isoforms were noted in human prostate cancer cell lines. Taken together, these results suggest a mechanism by which loss of PTEN may promote prostate cancer progression via PDGF D/β-PDGFR signal transduction.

MicroRNA-155 As a Potential Plasma Biomarker for Chronic Lymphocytic Leukemia and Waldenstrom Macroglobulinemia,

Abstract 3669 BackgroundMicroRNAs (miRNAs) are short, non-coding RNA molecules that average 18–24 nucleotides long and act as important post-transcriptional regulators. It has been demonstrated that miRNAs stably circulate in the blood and can be detected in plasma and serum. Numerous disease states, including both solid tumor and hematologic malignancies, have been shown to release miRNAs into the circulation. Furthermore, these tumor cells possess their own characteristic expression patterns of miRNAs. This presents an opportunity for specific miRNAs to serve as biomarkers for different diseases. Previous studies have shown microRNA-155 (miR-155) to be elevated in low grade lymphomas such as Chronic Lymphocytic Leukemia (CLL) and Waldenstrom Macroglobulinemia (WM). Currently, an established biomarker for diagnostic or prognostic applications does not exist for these diseases. In our study, we investigate miR-155 as a potential biomarker for CLL and WM in plasma. MethodsBoth plasma and serum samples were collected from CLL patients, WM patients, and healthy individuals. In order to quantify miR-155 levels, 100 μl of each sample went through a round of RNA isolation, reverse transcription (RT) reaction, and real-time quantitative PCR (qPCR) by using miRNeasy mini kit (Qiagen), Taqman microRNA reverse transcription kit (Applied Biosystem) and RT2 Fast SYBR® Green/ROX qPCR Master Mixes (SABiosciences). Based on the RT-qPCR results, samples were classified as having either detectable miR-155 (Ct value less than 40) or undetectable miR-155 (Ct value more than 40). The ratio of detectable to undetectable samples was used to compare groups of samples: i) CLL plasma, ii) CLL serum, iii) WM plasma, iv) WM serum v) Normal plasma, and vi) Normal serum. To adjust for variations in efficiency of RNA extraction among samples, C. elegans synthetic microRNA-39 was added specifically after denaturation of the sample and used as a spiked-in control. By using the CD63 antigen as a marker, exosomes in the plasma and serum were also detected through flow cytometry. ResultsA total of 20 CLL plasma samples showed a 100% positive ratio of detectable miR-155 while 20 CLL serum samples had only a 50% positive ratio. In addition, a total of 96 WM plasma samples had a positive ratio of 74% while 30 WM serum samples showed a much lower positive ratio of 3%. Of these 96 samples, 13 were obtained from upfront WM patients while 83 were from relapsed/refractory WM patients. The 10 plasma and 10 serum samples from healthy individuals were all negative for miR-155. Lastly, preliminary data indicated that a higher level of exosomes may exist in plasma compared to serum. SummaryThis finding suggests that miR-155 in peripheral blood plasma could potentially be used as a clinical biomarker for WM and/or CLL. The considerable difference in detectable miR-155 between patient plasma and serum was unexpected. Reasons for this disparity are still under investigation. Our preliminary data indicated that this may be due to a difference in exosomes, which are known to carry miRNAs, between plasma and serum. Ultimately, further investigation is warranted within a larger cohort to confirm the status of miR-155 as a reliable plasma biomarker for these low grade B cell malignancies. Disclosures:Roccaro:Roche. Ghobrial:Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Millennium: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Bristol-Myers Squibb: Research Funding; Noxxon: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding.

Abstract C13: Human Eag1 potassium channel expression in lung cancer biopsies.

Abstract Introduction. Lung cancer is the most common malignancy in the world including Mexico [1, 2]. Smoking is the main risk factor for the development of different types of lung cancer, about 70–80% of lung cancer cases are associated with smoking and approximately 50% of new cancer cases are diagnosed in ex-smokers. Current therapies rarely cure the disease, and the high relapse rate with the delay in diagnosis results in a poor prognosis and overall survival rates of 10% [1]. Several ion channels are over-expressed in cancer including Kv1.3, K2p9.1, Kv10.1 (Eag1) and Kv11.1 (HERG) channels. These channels are expressed in different cell types and tumor tissues and have been shown to increase cell proliferation. Eag1 is expressed aberrantly with a high frequency (75%) in tumor cells of different histological origins including sarcomas, carcinomas of the breast, colon, and cervix. Eag1 inhibition by either astemizole, imipramine, or Eag1 specific monoclonal antibodies reduces tumor cell proliferation in vitro and in vivo [3, 4, 5]. Eag1 channels are over-expressed in lung cancer [6]. However, a detailed study of Eag1 expression in the different types of lung cancer is missing. Materials and Methods: Lung biopsies: 44 Lung biopsies were obtained from patients attending the Instituto Nacional de Enfermedades Respiratorias (National Institute for Respiratory Diseases) in Mexico City following local ethical considerations. Patients had no prior treatment (chemotherapy or radiotherapy). 37 biopsies were classified as lung cancer samples and included adenocarcinoma, epidermoid, small cell, adenosquamous and neuroendocrine tumors. 5 samples were diagnosed as inflammatory disease and 2 were form patients with thyroid carcinoma. RNA extraction was performed with TRIzol (Life Technologies, Invitrogene) according to the manufacturer's recommendation. cDNA was synthesized by reverse transcription under the manufacturer's recommendations (New England BioLabs). Eag1 gene expression was assessed by real-time PCR under the manufacturer's recommendations (Fermentas SYBR Green/ROX qPCR Master Mix). Eag1 expression in lung biopsies was compared to Eag1 basal expression in fibroblasts from normal lung (WI-38) which was given the value of 1. Results: Eag1 expression was found in 81% of the cancer biopsies while 8% of the samples did not showed changes and in 10% of the biopsies Eag1 was found to be under-expressed. Interestingly, Eag1 was over-expressed in 80% of the samples from chronic inflammation while no changes were observed in the samples from thyroid carcinoma. Conclusions: Our results suggest Eag1 as a tumor marker for different types of lung cancer and as a potential early marker of the disease.

Low-Dose-Rate, Low-Dose Irradiation Delays Neurodegeneration in a Model of Retinitis Pigmentosa

The existence of radiation hormesis is controversial. Several stimulatory effects of low-dose (LD) radiation have been reported to date; however, the effects on neural tissue or neurodegeneration remain unknown. Here, we show that LD radiation has a neuroprotective effect in mouse models of retinitis pigmentosa, a hereditary, progressive neurodegenerative disease that leads to blindness. Various LD radiation doses were administered to the eyes in a retinal degeneration mouse model, and their pathological and physiological effects were analyzed. LD gamma radiation in a low-dose-rate (LDR) condition rescues photoreceptor cell apoptosis both morphologically and functionally. The greatest effect was observed in a condition using 650 mGy irradiation and a 26 mGy/minute dose rate. Multiple rounds of irradiation strengthened this neuroprotective effect. A characteristic up-regulation (563%) of antioxidative gene peroxiredoxin-2 (Prdx2) in the LDR-LD-irradiated retina was observed compared to the sham-treated control retina. Silencing the Prdx2 using small-interfering RNA administration reduced the LDR-LD rescue effect on the photoreceptors. Our results demonstrate for the first time that LDR-LD irradiation has a biological effect in neural cells of living animals. The results support that radiation exhibits hormesis, and this effect may be applied as a novel therapeutic concept for retinitis pigmentosa and for other progressive neurodegenerative diseases regardless of the mechanism of degeneration involved.

MYC Protein Inhibits Transcription of the MicroRNA Cluster MC-let-7a-1∼let-7d via Noncanonical E-box

The human microRNA cluster MC-let-7a-1∼let-7d, with three members let-7a-1, let-7f-1, and let-7d, is an important cluster of the let-7 family. These microRNAs play critical roles in regulating development and carcinogenesis. Therefore, precise control of MC-let-7a-1∼let-7d level is critical for cellular functions. In this study, we first showed that the expression of these three members was significantly reduced in human hepatocellular carcinoma HepG2 cells as compared with the immortalized human liver L02 cells. We demonstrated that the MC-let-7a-1∼let-7d cluster was encoded by a single polycistronic transcript driven by a 10-kb upstream promoter, with two MYC-binding sites. Importantly, MYC inhibited MC-let-7a-1∼let-7d promoter activity via binding to the noncanonical E-box 3 downstream of the transcription start sites, whereas it enhanced promoter activity by binding to the canonical E-box 2 upstream of the transcription start sites. We found that although the binding affinity of MYC to E-box 2 was stronger than E-box 3, the binding quantum of MYC to E-box 3 was significantly higher in cancerous HepG2 cells as compared with the noncancerous L02 cells. In addition, forced expression of let-7 could reverse the MYC-mediated cell proliferation. These findings suggested that in L02 cells with a low level of MYC, MYC binds mainly to E-box 2 to enhance MC-let-7a-1∼let-7d expression. However, in HepG2 cells with an elevated MYC, the extra MYC could bind to E-box 3 to suppress the transcription of MC-let-7a-1∼let-7d and thus enable HepG2 cells to maintain a high level of MYC and a low level of let-7 microRNAs simultaneously.

Bortezomib-resistant nuclear factor κB expression in stem-like cells in mantle cell lymphoma

Mantle cell lymphoma (MCL) is a subtype of B-cell Non-Hodgkin's Lymphoma (NHL) and accounts for approximately 6% of all lymphomas. Unlike small lymphocytic lymphoma and chronic lymphocytic lymphoma, which are relatively sensitive to chemotherapy, MCL is highly refractory to most chemotherapy, and has the worst survival rate among NHL patients. Stem-like cells in MCL, which we have termed mantle cell lymphoma-initiating cells (MCL-ICs), enriched in the population that are lack of prototypic B-cell marker CD19. These cells were able to self-renew upon serial transplantation and are highly tumorigenic. Importantly, these stem-like cells confer chemotherapeutic resistance to MCL. In this report, we show that stem-like MCL-ICs are resistant to bortezomib, as well as chemotherapeutic regimens containing bortezomib, despite constitutive nuclear factor-κB (NF-κB) expression. Interestingly, bortezomib treatment induced MCL-IC differentiation in plasma-like cells with upregulated expression of CD38 and CD138. This process was accompanied by expression of plasma cell differentiation transcriptional factors, BLIMP-1 and IRF4. This article is the first to show that stem-like MCL cells utilize constitutive NF-κB expression for survival. Given that the NF-κB expression in MCL-ICs is resistant to bortezomib, it will be important to find alternative therapeutic strategies to inhibit NF-κB expression.

Recruitment of SWI/SNF Complex Is Required for Transcriptional Activation of the SLC11A1 Gene during Macrophage Differentiation of HL-60 Cells

The solute carrier family 11 member 1 (SLC11A1) gene is strictly regulated and exclusively expressed in myeloid lineage cells. However, little is known about the transcriptional regulation of the SLC11A1 gene during myeloid development. In this study, we used HL-60 cells as a model to investigate the regulatory elements/factors involved in the transactivation of the SLC11A1 gene during phorbol 12-myristate 13-acetate (PMA)-induced macrophage differentiation of HL-60 cells. Promoter deletion analysis showed that a 7-base AP-1-like element (TGACTCT) was critical for the responsiveness of the SLC11A1 promoter to PMA. Stimulation by PMA induced the binding of ATF-3 and the recruitment of two components of the SWI/SNF complex, BRG1 and β-actin, to this element in an ATF-3-dependent manner. RNAi-mediated depletion of ATF-3 or BRG1 markedly decreased SLC11A1 gene expression and its promoter activity induced by PMA. Luciferase reporter experiments demonstrated that ATF-3 cooperated with BRG1 and β-actin to activate the SLC11A1 promoter. Furthermore, we showed that PMA can induce the proximal (GT/AC)(n) repeat sequence to convert to the Z-DNA structure in the SLC11A1 gene promoter, and depletion of BRG1 resulted in a significant decrease of Z-DNA formation. Our results demonstrated that recruitment of the SWI/SNF complex initiated Z-DNA formation and subsequently helped to transactivate the SLC11A1 gene.

Structural and Functional Analysis of Tomosyn Identifies Domains Important in Exocytotic Regulation

Tomosyn is a 130-kDa cytosolic R-SNARE protein that associates with Q-SNAREs and reduces exocytotic activity. Two paralogous genes, tomosyn-1 and -2, occur in mammals and produce seven different isoforms via alternative splicing. Here, we map the structural differences between the yeast homologue of m-tomosyn-1, Sro7, and tomosyn genes/isoforms to identify domains critical to the regulation of exocytotic activity to tomosyn that are outside the soluble N-ethylmaleimide-sensitive attachment receptor motif. Homology modeling of m-tomosyn-1 based on the known structure of yeast Sro7 revealed a highly conserved functional conformation but with tomosyn containing three additional loop domains that emanate from a β-propeller core. Notably, deletion of loops 1 and 3 eliminates tomosyn inhibitory activity on secretion without altering its soluble N-ethylmaleimide-sensitive attachment receptor pairing with syntaxin1A. By comparison, deletion of loop 2, which contains the hypervariable splice region, did not reduce the ability of tomosyn to inhibit regulated secretion. However, exon variation within the hypervariable splice region resulted in significant differences in protein accumulation of tomosyn-2 isoforms. Functional analysis of s-tomosyn-1, m-tomosyn-1, m-tomosyn-2, and xb-tomosyn-2 demonstrated that they exert similar inhibitory effects on elevated K(+)-induced secretion in PC12 cells, although m-tomosyn-2 was novel in strongly augmenting basal secretion. Finally, we report that m-tomosyn-1 is a target substrate for SUMO 2/3 conjugation and that mutation of this small ubiquitin-related modifier target site (Lys-730) enhances m-tomosyn-1 inhibition of secretion without altering interaction with syntaxin1A. Together these results suggest that multiple domains outside the R-SNARE of tomosyn are critical to the efficacy of inhibition by tomosyn on exocytotic secretion.