Detection Of mRNA Transcripts Research Articles

RNaseH-based ribodepletion of total planarian RNA improves detection of longer and non-polyadenylated transcripts.

The overwhelming majority of RNA species isolated from cells or tissues using organic extraction are ribosomal RNAs (rRNA), whereas a relatively small percentage are messenger RNAs (mRNA). For studies that seek to detect mRNA transcripts and measure changes in their expression, this lopsided ratio of desired transcripts to undesired transcripts creates a significant challenge to obtaining sensitive and reproducible results. One method for improving mRNA detection is to selectively amplify polyadenylated (polyA) mRNA molecules when generating RNA-seq libraries, a strategy that is generally very successful in many species. However, this strategy is less effective when starting with total RNA from some species e.g., the planarian species Schmidtea mediterranea (S.med), as it generates libraries that still contain significant and variable amounts of rRNA reads. Further, commercially available ribodepletion kits do not efficiently deplete rRNAs from these samples because their sequences are divergent from mammalian rRNAs. Here we report a customized, optimized, and economical ribodepletion strategy than allows the generation of comprehensive RNA-seq libraries with less than one percent rRNA contamination. We show that this method improves transcript detection, particularly for those without polyA tails (e.g., core histones) and those that are relatively long (e.g., microtubule motor proteins). Using this custom ribodepletion approach, we also detected many transcripts that are not represented in the most recent set of S.med gene annotations, including a subset that are likely expressed transposable elements (TEs). To facilitate future differential expression analyses of these newly identified loci, we created both an annotation file of the new loci we identified and a bioinformatic pipeline for generating additional annotations from future libraries. As significant recent research shows that TE activation is regulated and functionally important, the resources provided here will provide a starting point for investigating such mechanisms in planarians and other species with less conserved rRNA sequences.

Molecular profiling of CO2/pH-sensitive neurons in the locus coeruleus of bullfrogs reveals overlapping noradrenergic and glutamatergic cell identity

Locus coeruleus (LC) neurons regulate breathing by sensing CO2/pH. Neurons within the vertebrate LC are the main source of norepinephrine within the brain. However, they also use glutamate and GABA for fast neurotransmission. Although the amphibian LC is recognized as a site involved in central chemoreception for the control of breathing, the neurotransmitter phenotype of these neurons is unknown. To address this question, we combined electrophysiology and single-cell quantitative PCR to detect mRNA transcripts that define norepinephrinergic, glutamatergic, and GABAergic phenotypes in LC neurons activated by hypercapnic acidosis (HA) in American bullfrogs. Most LC neurons activated by HA had overlapping expression of noradrenergic and glutamatergic markers but did not show strong support for GABAergic transmission. Genes that encode the pH-sensitive K+ channel, TASK2, and acid-sensing cation channel, ASIC2, were most abundant, while Kir5.1 was present in 1/3 of LC neurons. The abundance of transcripts related to norepinephrine biosynthesis linearly correlated with those involved in pH sensing. These results suggest that noradrenergic neurons in the amphibian LC also use glutamate as a neurotransmitter and that CO2/pH sensitivity may be linkedto the noradrenergic cell identity.

Quantified integrated hepatitis B virus is related to viral activity in patients with chronic hepatitis B.

Background and AimsHBV can integrate in the host genome of the hepatocyte and recent findings suggest that integrated HBV contributes to the persistent production of viral proteins. Here, we quantified the levels of integrated HBV in patients with chronic hepatitis B (CHB) and analyzed the relation between HBV integration, virological activity (plasma HBV DNA and HBsAg levels), and clinical outcomes.Approach and ResultsWe developed and validated a multistep Arthrobacter luteus (Alu)‐PCR that specifically amplifies integrated HBV and RT‐Alu‐PCR detecting mRNA transcripts derived from integrated HBV. Pretreatment liver biopsy samples and baseline characteristics of 124 patients with CHB either treated for 48 weeks with pegylated interferon plus adefovir or tenofovir or receiving no treatment were available for analysis. Integrated HBV sequences containing open reading frame S and X (but not C) and S and X mRNA transcripts derived from integrated HBV could be detected and quantified in liver biopsies. Integrated HBV levels correlated with HBV DNA, HBsAg, alanine aminotransferase plasma levels, and the liver histology activity index but not to levels of intrahepatic covalently closed circular DNA (cccDNA), plasma pregenomic RNA, or hepatitis B core‐related antigen. Multivariable logistic regression analysis showed that lower baseline HBV integration levels were independently associated with HBsAg loss (functional cure) within 5 years follow‐up.ConclusionsIntegrated HBV levels are strongly correlated with surrogate markers for virological activity but not to cccDNA levels and are predictive for HBsAg loss. Our data suggest that integrated HBV is closely related to HBV replication and may therefore be an important tool in the evaluation and development of treatment modalities aiming to cure CHB.

Sparcle: assigning transcripts to cells in multiplexed images.

Imaging-based spatial transcriptomics has the power to reveal patterns of single-cell gene expression by detecting mRNA transcripts as individually resolved spots in multiplexed images. However, molecular quantification has been severely limited by the computational challenges of segmenting poorly outlined, overlapping cells and of overcoming technical noise; the majority of transcripts are routinely discarded because they fall outside the segmentation boundaries. This lost information leads to less accurate gene count matrices and weakens downstream analyses, such as cell type or gene program identification. Here, we present Sparcle, a probabilistic model that reassigns transcripts to cells based on gene covariation patterns and incorporates spatial features such as distance to nucleus. We demonstrate its utility on both multiplexed error-robust fluorescence in situ hybridization, single-molecule FISH data, probabilistic cell typing in situ sequencing, spatially resolved transcript amplicon readout mapping and MERFISH from Vizgen. Sparcle improves transcript assignment, providing more realistic per-cell quantification of each gene, better delineation of cell boundaries and improved cluster assignments. Critically, our approach does not require an accurate segmentation and is agnostic to technological platform. The code is available at: https://github.com/sandhya212/Sparcle_for_spot_reassignments. sandhya.prabhakaran@moffitt.org. Supplementary data are available at Bioinformatics Advances online.

Angiotensin II and Angiotensin‐(1‐7) Modulate Mitochondrial Respiration in Mouse Mesenchymal Stromal Cells

Mesenchymal stromal cells (MSCs) constitute bone marrow niches that support homing and quiescence of hematopoietic stem cells via paracrine functions. MSCs have the potential of differentiating into a variety of cell types and therefore have therapeutic potential in regenerative medicine. Mitochondria modulates cellular functions including paracrine functions by which MSCs modulate quiescence and differentiation of stem cells. Previous studies have provided evidence for the expression of renin-angiotensin system in MSCs. The current study evaluated the effects of Angiotensin II (Ang II) and Angiotensin-(1-7) (Ang-(1-7)) on mitochondrial respiration in mouse bone marrow MSCs. Study was carried out in cultured MSCs, passage eight or nine, and mitochondrial respiration was evaluated by using Seahorse (XFp). Expression of ACE, ACE2, AT1R, AT2R and Mas receptor were evaluated by real-time PCR and western blotting. Oxygen consumption rate (OCR) was determined by carrying out mito-stress test. For measuring OCR in real-time, the mito-stress test was carried out, which involved use of different pharmacological agents that modulate mitochondrial electron transport chain such as oligomycin (2µm), FCCP (0.5µm), rotenone/ antimycin A (0.5µm) to determine ATP-linked respiration, maximal respiration, non-mitochondrial respiration, respectively, after recording basal respiration. PCR detected mRNA transcripts of ACE, AT1R, AT2R, and Mas, but not ACE2. Mito-stress test showed dose-dependent (0.1nm, 1nm, 10nm) increase in basal, ATP-linked, maximal, and nonmitochondrial respiration by Ang-(1-7) and effects at 10nm concentration were significant (P<0.05, n=5) compared to the untreated cells (Figure 1). All these changes were blocked by A-779 (1µm). All of the mitochondrial respiratory parameters were significantly (P<0.05, n=5) decreased when only A-779 was present compared to untreated cells. Ang II (100nm) did not alter OCR in MSCs in mito-stress test (Figure 1). Proton leak was not changed by any treatments. Intriguingly, treatment with PD123391 (1µm) significantly increased basal respiration and maximal respiration compared to untreated cells (P<0.05). These effects were not observed when cells were treated with Ang II along with PD123391. Along similar lines, losartan (10µm) significantly increased the basal respiration compared to untreated MSCs (P<0.05), and this change was not observed in the presence of Ang II. This preliminary study shows that mitochondrial oxygen consumption in MSCs is differentially modulated by angiotensin peptides. Further investigations are needed to address the significance of mitochondrial modulation in the regenerative functions of MSCs by angiotensins.

Investigation of a 24-Hour Culture Step to Determine the Viability of Streptococcus equi Subspecies equi Via Quantitative Polymerase Chain Reaction in Nasal Secretions From Horses With Suspected Strangles

Polymerase chain reaction (PCR)–based detection assays for Streptococcus equi subspecies equi often overestimate the prevalence of samples containing viable organisms. The objective of this study was to determine if viability could be determined using genome quantitation and detection of messenger RNA (mRNA) transcripts for the SeM gene of S. equi in pre- and post-cultured samples. Nasal secretions collected from 42 horses with suspected strangles were tested by culture and by quantitative PCR (qPCR) before and 24 hours after a culture step. Viable S. equi was determined based on the detection of S. equi via culture, the detection of mRNA transcripts for the SeM gene of S. equi by qPCR, and/or an increase in absolute number of SeM target genes of S. equi between pre- and post-cultured samples. Viability was determined in 28/42 samples based on isolation of S. equi (11 samples), the presence of mRNA transcripts for the SeM gene of S. equi (25), and/or an increase in absolute quantitation of the SeM gene of S. equi between pre- and post-culture (17). The overall agreement between culture alone and the three criteria to determine viability was 59%. The overall agreement for the detection of mRNA transcripts and increase in absolute target genes was 88% and 74%, respectively. The combination of mRNA transcripts and increase in absolute target genes was able to determine the viability status in all 42 samples. In the absence of a culture-positive result for S. equi, the determination of viability can be achieved by using molecular strategies applied to samples undergoing a 24-hour culture step.

Expression and subcellular analyses of CCR8a/b genes with the identification of response to SGIV viral infect in orange-spotted grouper (Epinephelus coioides)

Chemokine receptors are a superfamily of seven transmembrane domain G-coupled receptors, and they play important roles in immune surveillance, inflammation, and development. Recently, nine CC chemokine receptors (CCRs) were identified and cloned from orange-spotted grouper (Epinephelus coioides) and annotated by phylogenetic and syntenic analyses. We detected mRNA transcripts for CCRs in healthy tissues of E. coioides, and CCR genes were highly expressed in the immune-relevant tissues. Analysis of gene expression after Singapore grouper iridovirus (SGIV) infection indicated that CCR genes are regulated in a gene-specific manner. CCR8a and CCR8b were significantly upregulated in the spleen and liver of resistant fish, indicating potential roles in immunity against the pathogen. Fluorescence microscopy revealed that CCR8a and CCR8b were expressed predominantly in the cytoplasm. Overexpression of CCR8a and CCR8b in grouper cells significantly inhibited the replication of SGIV, demonstrating that they delayed the occurrence of cytopathic effects induced by SGIV infection and inhibited viral gene transcription. CCR8a and CCR8b overexpression also significantly increased the expression of interferon (IFN)-related cytokines and activated IFN response element and IFN promoter activities. These results demonstrated that CCR8a and CCR8b might have an antiviral function against SGIV infect.

Packaging functionally important plasma proteins into the α-granules of human-induced pluripotent stem cell-derived megakaryocytes.

The contents of platelet α-granules arrive via a number of pathways; some are synthesized by megakaryocytes (MKs), for example, von Willebrand factor (VWF), whereas others are endocytosed from plasma, for example, fibrinogen (Fgn) and factor V (FV). Currently, almost all in vitro-induced pluripotent stem cell (iPSC)-derived MKs are generated under serum-free conditions, and their α-granule cargoes lack components that would normally be taken up from plasma during the course of megakaryopoiesis. How this might affect the ability of in vitro-derived platelets to contribute fully to haemostasis is not known. The purpose of this investigation was to examine whether "feeding" human plasma to iPSC-derived MKs might result in loading their α-granules with physiologically important proteins. iPSCs were differentiated to CD41+ /CD42b+ MKs using a serum-free protocol. The resulting MKs were polyploid, expressed a number of platelet-specific surface receptors, and spread on Fgn or collagen-coated surfaces. Reverse transcription-polymerase chain reaction analysis detected mRNA transcripts for FV and VWF but not Fgn chains. Fluorescence immunocytochemistry and confocal microscopy confirmed constitutive VWF distribution in granule-like structures in MKs cultured under plasma-free conditions, and the granules became positive for Fgn upon incubation with human plasma. iPSC-derived MKs showed a low level of constitutive FV expression that increased dramatically upon incubation with human plasma. Taken together, these data suggest that human iPSC-derived MKs are capable of endocytosing and storing plasma components in their α-granules. Incorporating this methodology into current protocols for producing in vitro-derived MKs should provide novel insights into MK biology and lead to the generation of large numbers of MKs and platelets with improved functionality.

The CXC chemokines and CXC chemokine receptors in orange-spotted grouper (Epinephelus coioides) and their expression after Singapore grouper iridovirus infection

Chemokines comprise a group of small molecular weight (6–14 kDa) cytokines; chemokine receptors are a superfamily of seven transmembrane domain G-coupled receptors. Both chemokines and their receptors have important roles in immune surveillance, inflammation, and development. Recently, 9 CXC chemokine ligands (CXCLs) and 8 CXC chemokine receptors (CXCRs) were identified and cloned from orange-spotted grouper (Epinephelus coioides) and annotated by phylogenetic and syntenic analyses. We detected mRNA transcripts for CXCLs and CXCRs in healthy tissues of E. coioides. Our data show that CXCL genes are highly expressed in the spleen, kidney and liver and that CXCR genes are ubiquitously expressed, rather than being expressed only in immune organs. Analysis of gene expression after Singapore grouper iridovirus infection indicated that CXCL and CXCR genes are regulated in a gene-specific manner. CXCL8 and CXCL12a were significantly upregulated in the spleen, kidney and liver of resistant fish, indicating potential roles in immunity against the pathogen. Additionally, CXCR4a was upregulated in all three organs in resistant fish, suggesting that CXCL8 or CXCL12a may participate in the immune response via interaction with CXCR4a. In addition, the new orange-spotted grouper receptor CXCR1b was found to be upregulated in the spleen and kidney of resistant fish, indicating that this receptor plays an important role in immune responses to viral infection. These results are valuable for comparative immunological studies and provide insight into the roles of these genes in viral infection.

Identification of Surface Protein Biomarkers of Listeria monocytogenes via Bioinformatics and Antibody-Based Protein Detection Tools.

The Gram-positive bacterium Listeria monocytogenes causes a significant percentage of the fatalities among foodborne illnesses in humans. Surface proteins specifically expressed in a wide range of L. monocytogenes serotypes under selective enrichment culture conditions could serve as potential biomarkers for detection and isolation of this pathogen via antibody-based methods. Our study aimed to identify such biomarkers. Interrogation of the L. monocytogenes serotype 4b strain F2365 genome identified 130 putative or known surface proteins. The homologues of four surface proteins, LMOf2365_0578, LMOf2365_0581, LMOf2365_0639, and LMOf2365_2117, were assessed as biomarkers due to the presence of conserved regions among strains of L. monocytogenes which are variable among other Listeria species. Rabbit polyclonal antibodies against the four recombinant proteins revealed the expression of only LMOf2365_0639 on the surface of serotype 4b strain LI0521 cells despite PCR detection of mRNA transcripts for all four proteins in the organism. Three of 35 monoclonal antibodies (MAbs) to LMOf2365_0639, MAbs M3643, M3644, and M3651, specifically recognized 42 (91.3%) of 46 L. monocytogenes lineage I and II isolates grown in nonselective brain heart infusion medium. While M3644 and M3651 reacted with 14 to 15 (82.4 to 88.2%) of 17 L. monocytogenes lineage I and II isolates, M3643 reacted with 22 (91.7%) of 24 lineage I, II, and III isolates grown in selective enrichment media (UVM1, modified Fraser, Palcam, and UVM2 media). The three MAbs exhibited only weak reactivities (the optical densities at 414 nm were close to the cutoff value) to some other Listeria species grown in selective enrichment media. Collectively, the data indicate the potential of LMOf2365_0639 as a surface biomarker of L. monocytogenes, with the aid of specific MAbs, for pathogen detection, identification, and isolation in clinical, environmental, and food samples. L. monocytogenes is traditionally divided into at least 12 serotypes. Currently, there are no monoclonal antibodies (MAbs) available that are capable of binding to the surface of L. monocytogenes strains representing all 12 serotypes. Such antibodies would be useful and are needed for the development of methods to detect and isolate L. monocytogenes from food samples. In our study, we aimed to identify surface proteins that possess regions of well-conserved amino acid sequences among various serotypes and then to employ them as antigen targets (biomarkers) for the development of MAbs. Through bioinformatics and protein expression analysis, we identified one of the four putative surface protein candidates, LMOf2365_0639, encoded by the genome of the L. monocytogenes serotype 4b strain F2365, as a useful surface biomarker. Extensive assessment of 35 MAbs raised against LMOf2365_0639 in our study revealed three MAbs (M3643, M3644, and M3651) that recognized a wide range of L. monocytogenes isolates.

Novel regulatory mechanism in human urinary bladder: central role of transient receptor potential melastatin 4 channels in detrusor smooth muscle function.

Transient receptor potential melastatin 4 (TRPM4) channels are Ca(2+)-activated nonselective cation channels that have been recently identified as regulators of detrusor smooth muscle (DSM) function in rodents. However, their expression and function in human DSM remain unexplored. We provide insights into the functional role of TRPM4 channels in human DSM under physiological conditions. We used a multidisciplinary experimental approach, including RT-PCR, Western blotting, immunohistochemistry and immunocytochemistry, patch-clamp electrophysiology, and functional studies of DSM contractility. DSM samples were obtained from patients without preoperative overactive bladder symptoms. RT-PCR detected mRNA transcripts for TRPM4 channels in human DSM whole tissue and freshly isolated single cells. Western blotting and immunohistochemistry with confocal microscopy revealed TRPM4 protein expression in human DSM. Immunocytochemistry further detected TRPM4 protein expression in DSM single cells. Patch-clamp experiments showed that 9-phenanthrol, a selective TRPM4 channel inhibitor, significantly decreased the transient inward cation currents and voltage step-induced whole cell currents in freshly isolated human DSM cells. In current-clamp mode, 9-phenanthrol hyperpolarized the human DSM cell membrane potential. Furthermore, 9-phenanthrol attenuated the spontaneous phasic, carbachol-induced and nerve-evoked contractions in human DSM isolated strips. Significant species-related differences in TRPM4 channel activity between human, rat, and guinea pig DSM were revealed, suggesting a more prominent physiological role for the TRPM4 channel in the regulation of DSM function in humans than in rodents. In conclusion, TRPM4 channels regulate human DSM excitability and contractility and are critical determinants of human urinary bladder function. Thus, TRPM4 channels could represent promising novel targets for the pharmacological or genetic control of overactive bladder.

Molecular cloning and characterization of orange-spotted grouper (Epinephelus coioides) CXC chemokine ligand 12.

Chemokines are a family of soluble peptides that can recruit a wide range of immune cells to sites of infection and disease. The CXCL12 is a chemokine that binds to its cognate receptor CXCR4 and thus involved in multiple physiological and pathophysiological processes. In this study, we cloned and characterized CXCL12 from Epinephelus coioides (osgCXCL12). We found that the open reading frame of osgCXCL12 consists of 98 amino acid residues with the small cytokine C-X-C domain located between residues 29 and 87. Higher expression levels for osgCXCL12 were detected at the kitting stage, compared with the prolarva and larva shape stages. The expression patterns revealed that osgCXCL12 may play a key role in early grouper development. We detected mRNA transcripts for osgCXCL12 in healthy tissues and found the highest osgCXCL12 expression in the head kidney. Furthermore, a time-course analysis revealed significantly increased osgCXCL12 and osgCXCR4 expression levels after the nervous necrosis virus (NNV) challenge. In addition, expression of osgCXCL12 was affected by injection with microbial mimics [LPS and poly(I:C)]. These results suggest that osgCXCL12 is associated with inflammatory and developmental processes in the grouper.

Degraded RNA transcript stable regions (StaRs) as targets for enhanced forensic RNA body fluid identification

The detection of messenger RNA (mRNA) using reverse transcriptase PCR (RT-PCR) is becoming common practice for forensic body fluid identification. However, the degraded and scarce nature of RNA from forensic samples mean that mRNA transcripts are not consistently detected or remain undetected in practice. Conventional primer design for RT-PCR (and quantitative RT-PCR) includes targeting primers to span exon–exon boundaries or by having the primers on two separate exons, and satisfying common primer thermodynamic criteria. We have found that the conventional placement of primers is not always optimal for obtaining reproducible results from degraded samples. Using massively parallel sequencing data from degraded body fluids, we designed primers to amplify transcript regions of high read coverage, hence, higher stability, and compared these with primers designed using conventional methodology. Our findings are that primers designed for transcript regions of higher read coverage resulted in vastly improved detection of mRNA transcripts that were not previously detected or were not consistently detected in the same samples using conventional primers. We developed a new concept whereby primers targeted to transcript stable regions (StaRs) are able to consistently and specifically amplify a wide range of RNA biomarkers in various body fluids of varying degradation levels.

Slc26a3/Dra and Slc26a6 in Murine Ameloblasts

Formation of apatite crystals during enamel development generates protons. To sustain mineral accretion, maturation ameloblasts need to buffer these protons. The presence of cytosolic carbonic anhydrases, the basolateral Na+ bicarbonate cotransporter Nbce1, and the basolateral anion exchanger Ae2a,b in maturation ameloblasts suggests that these cells secrete bicarbonates into the forming enamel, but it is unknown by which mechanism. Solute carrier (Slc) family 26A encodes different anion exchangers that exchange Cl–/HCO3–, including Slc26a3/Dra, Slc26a6/Pat-1, and Slc26a4/pendrin. Previously, we showed that pendrin is expressed in ameloblasts but is not critical for enamel formation. In this study, we tested the hypothesis that maturation ameloblasts express Dra and Slc26a6 to secrete bicarbonate into the enamel space in exchange for Cl–. Real-time polymerase chain reaction detected mRNA transcripts for Dra and Slc26a6 in mouse incisor enamel organs, and Western blotting confirmed their translation into protein. Both isoforms were immunolocalized in ameloblasts, principally at maturation stage. Mice with null mutation of either Dra or Slc26a6 had a normal dental or skeletal phenotype without changes in mineral density, as measured by micro–computed tomography. In enamel organs of Slc26a6-null mice, Dra and pendrin protein levels were both elevated by 52% and 55%, respectively. The amount of Slc26a6 protein was unchanged in enamel organs of Ae2a,b- and Cftr-null mice but reduced in Dra-null mice by 36%. Our data show that ameloblasts express Dra, pendrin, or Slc26a6 but each of these separately is not critical for formation of dental enamel. The data suggest that in ameloblasts, Slc26a isoforms can functionally compensate for one another.

Abstract LB-280: Gene expression profiling of individual circulating tumor cells from non-small cell lung cancer (NSCLC) patients via integrated nanotechnologies

Abstract Background: Circulating tumor cells (CTCs), defined as epithelial cells shed from a primary tumor into the bloodstream, are valuable prognostic, and possibly diagnostic, biomarkers that contain actionable genetic information for cancer treatment. Unfortunately, the rarity of CTCs in comparison to other blood components necessitates high-throughput separation technologies for efficient enrichment and practical downstream analysis. Moreover, genetic data extraction from CTCs currently suffers from a dearth of reliable analytical methods capable of handling low cell numbers. Technological innovations are urgently required to developing platforms that can help to optimize cancer management. Aim: To measure gene expression profiles of individual CTCs for cancer management via an integrated nanoscale platform. Methods: We have developed a protocol to effectively enrich rare cells via a magnetic sifting technology, whose methodology is based on using magnetic nanoparticles to tag CTCs in conjunction with magnetic filtration to enable high-throughput enrichment with release capability. This magnetic sifter offers 1) high capture efficiency at fast flow rates due to extreme field gradients at the pore edges, 2) high throughput due to the density of pores (∼200 pores/mm2), 3) scalability via standard lithographic fabrication, and 4) harvesting of viable cells. For subsequent characterization, a robust nanowell-based assay was designed to circumvent experimental errors associated with ensemble measurements through detection of mRNA transcripts directly from single CTCs (using one-step RT-PCR). Using standard photolithography, 25,600 nanowells are positioned on top of polydimethyl-siloxane (PDMS) and designed for subsequent RT-PCR reaction from a single CTC. These massive single-cell arrays are able to isolate up to thousands of individual NSCLC cells to measure gene expression. Also, this device is easily interrogated by conventional fluorescence microscopy to detect a candidate panel of genes on CTCs that are relevant for cancer detection or therapy monitoring. Nanowell is innovative as a low-cost (PDMS-based), easily scalable (from currently 25k to more than 100k nanowells), adjunctive solution to existing diagnostic methods. Results and Discussion: To date, we have assayed 23 NSCLC patients using the MagSifter &amp; Nanowell and detected CTCs with valid biomarkers (hTERT and cMET). Each 4-mL whole blood sample was processed within one working day using the current workflow. From these samples, individual CTCs were assessed for hTERT and cMet expression. Single CTCs displaying hTERT only, cMet only, and both were evident upon fluorescent imaging. Direct comparison with CTC enumeration confirms better sensitivity by Nanowell assay, since the Nanowell utilizes PCR amplification in fluorescence as a signal generator. We believe this is the first demonstration of ex vivo visualization of gene expression from individual lung cancer CTCs. Citation Format: Seung-min Park, Dawson J. Wong, Chin Chun Ooi, Viswam S. Nair, Ophir Vermesh, Sang Hun Lee, Susie Suh, Luke P. Lee, Shan X. Wang, Sanjiv S. Gambhir. Gene expression profiling of individual circulating tumor cells from non-small cell lung cancer (NSCLC) patients via integrated nanotechnologies. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-280. doi:10.1158/1538-7445.AM2015-LB-280

Expression and effect of NAMPT (visfatin) on progesterone secretion in hen granulosa cells

In mammals, nicotinamide phosphoribosyltransferase (NAMPT) is an adipokine produced by adipose tissue that is found in intracellular and extracellular compartments. The intracellular form of NAMPT is a nicotinamide phosphoribosyltransferase, whereas the extracellular form is considered an adipokine. In humans, NAMPT regulates energy metabolism and reproductive functions, such as ovarian steroidogenesis. To date, no study has investigated the role of NAMPT in hen ovaries. We investigated whether NAMPT is present in hen ovarian follicles and its role in granulosa cells. Using RT-PCR, western blotting and immunocytochemistry, we detected mRNA transcripts and proteins related to NAMPT in theca and granulosa cells from pre-ovulatory follicles. Using RT-PCR, we demonstrated that mRNA NAMPT levels were higher in granulosa cells than they were in theca cells and that during follicle development, theca cell levels decreased, whereas levels remained unchanged in granulosa cells. NAMPT protein quantities were significantly higher in theca cells than they were in granulosa cells, but they were unchanged during follicular development. Plasma NAMPT levels, as determined by ELISA and immunoblotting, were significantly lower in adult hens than they were in juveniles. In vitro, treatment with human recombinant NAMPT (100 ng/ml, 48 h) halved basal and IGF1-induced progesterone secretion, and this was associated with a reduction in STAR and HSD3B protein levels and MAPK3/1 phosphorylation levels in granulosa cells. These effects were abolished by the addition of FK866, a specific inhibitor of NAMPT enzymatic activity. Moreover, NAMPT had no effect on granulosa cell proliferation. In conclusion, NAMPT is present in hen ovarian cells and inhibits progesterone production in granulosa cells.

Expression and Pharmacology of Endogenous Cav Channels in SH-SY5Y Human Neuroblastoma Cells

SH-SY5Y human neuroblastoma cells provide a useful in vitro model to study the mechanisms underlying neurotransmission and nociception. These cells are derived from human sympathetic neuronal tissue and thus, express a number of the Cav channel subtypes essential for regulation of important physiological functions, such as heart contraction and nociception, including the clinically validated pain target Cav2.2. We have detected mRNA transcripts for a range of endogenous expressed subtypes Cav1.3, Cav2.2 (including two Cav1.3, and three Cav2.2 splice variant isoforms) and Cav3.1 in SH-SY5Y cells; as well as Cav auxiliary subunits α2δ1–3, β1, β3, β4, γ1, γ4–5, and γ7. Both high- and low-voltage activated Cav channels generated calcium signals in SH-SY5Y cells. Pharmacological characterisation using ω-conotoxins CVID and MVIIA revealed significantly (∼ 10-fold) higher affinity at human versus rat Cav2.2, while GVIA, which interacts with Cav2.2 through a distinct pharmacophore had similar affinity for both species. CVID, GVIA and MVIIA affinity was higher for SH-SY5Y membranes vs whole cells in the binding assays and functional assays, suggesting auxiliary subunits expressed endogenously in native systems can strongly influence Cav2.2 channels pharmacology. These results may have implications for strategies used to identify therapeutic leads at Cav2.2 channels.

Concurrent Transcript and Protein Quantification in a Massive Single Cell Array Enables Population-Wide Observation of Oncogene Escape

The cancer stem cell (CSC) model focuses on the key role these cells can play in drug resistance, since CSCs are believed to reconstitute the cancer after intense chemotherapy treatment. In order to effectively identify and profile CSCs within a heterogeneous tumor population, we are investigating quantitative correlation of messenger RNAs and their translated proteins as a distinctive parameter of the CSC population. However, previous research on mRNA expression and protein abundance has shown the correlations between the two are weak or only “stochastically meaningful” due to the significant level of experimental error originating from ensemble observations. Here, we demonstrate a robust microwell-based method to minimize these errors by monitoring both mRNA expression and the corresponding protein abundance from individual cancer cells. Simultaneous observation of membrane protein expression by immunostaining and detection of mRNA transcripts directly from individual cells using a one-step, reverse transcription polymerase chain reaction have been integrated in a massive single-cell array platform. The proposed experimental scheme was initially tested and validated in three established lung cancer cell lines by correlating mRNA transcript and protein expression levels of individual cells and quantitation of heterogeneity. Responses at the individual cell level to known transcriptional and translational inhibitors, as well as to EGFR-specific inhibitors were evaluated, providing quantitative measures of the heterogeneous response of non-small cell lung cancer cells to the inhibitors. Results showed that drug-treated cell lines displayed oncogene escape due to expunction of drug-sensitive subpopulations in the cell lines. Furthermore, correlation of c-MET mRNA and protein levels revealed unique response patterns in different EGFR-mutated cell lines. Thus, these results demonstrate the potential for molecular profiling at the single cell level to prospectively identify the CSCs subpopulation for effective combinatorial treatments.

A model system for assessing and comparing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells

BackgroundMalignant cells in tumours of B-cell origin account for 0.1% to 98% of the total cell content, depending on disease entity. Recently, gene expression profiles (GEPs) of B-cell lymphomas based on microarray technologies have contributed significantly to improved sub-classification and diagnostics. However, the varying degrees of malignant B-cell frequencies in analysed samples influence the interpretation of the GEPs. Based on emerging next-generation sequencing technologies (NGS) like tag sequencing (tag-seq) for GEP, it is expected that the detection of mRNA transcripts from malignant B-cells can be supplemented. This study provides a quantitative assessment and comparison of the ability of microarrays and tag-seq to detect mRNA transcripts from malignant B-cells. A model system was established by eight serial dilutions of the malignant B-cell lymphoma cell line, OCI-Ly8, into the embryonic kidney cell line, HEK293, prior to parallel analysis by exon microarrays and tag-seq.ResultsWe identified 123 and 117 differentially expressed genes between pure OCI-Ly8 and HEK293 cells by exon microarray and tag-seq, respectively. There were thirty genes in common, and of those, most were B-cell specific. Hierarchical clustering from all dilutions based on the differentially expressed genes showed that neither technology could distinguish between samples with less than 1% malignant B-cells from non-B-cells. A novel statistical concept was developed to assess the ability to detect single genes for both technologies, and used to demonstrate an inverse proportional relationship with the sample purity. Of the 30 common genes, the detection capability of a representative set of three B-cell specific genes - CD74, HLA-DRA, and BCL6 - was analysed. It was noticed that at least 5%, 13% and 22% sample purity respectively was required for detection of the three genes by exon microarray whereas at least 2%, 4% and 51% percent sample purity of malignant B-cells were required for tag-seq detection.ConclusionA sample purity-dependent loss of the ability to detect genes for both technologies was demonstrated. Taq-seq, in comparison to exon microarray, required slightly less malignant B-cells in the samples analysed in order to detect the two most abundantly expressed of the selected genes. The results show that malignant cell frequency is an important variable, with fundamental impact when interpreting GEPs from both technologies.

High-Resolution Whole-MountIn SituHybridization Using Quantum Dot Nanocrystals

The photostability and narrow emission spectra of nanometer-scale semiconductor crystallites (QDs) make them desirable candidates for whole-mount fluorescent in situ hybridization to detect mRNA transcripts in morphologically preserved intact embryos. We describe a method for direct QD labeling of modified oligonucleotide probes through streptavidin-biotin and antibody-mediated interactions (anti-FITC and anti-digoxigenin). To overcome permeability issues and allow QD conjugate penetration, embryos were treated with proteinase K. The use of QDs dramatically increased sensitivity of whole-mount in situ hybridization (WISH) in comparison with organic fluorophores and enabled fluorescent detection of specific transcripts within cells without the use of enzymatic amplification. Therefore, this method offers significant advantages both in terms of sensitivity, as well as resolution. Specifically, the use of QDs alleviates issues of photostability and limited brightness plaguing organic fluorophores and allows fluorescent imaging of cleared embryos. It also offers new imaging possibilities, including intracellular localization of mRNAs, simultaneous multiple-transcript detection, and visualization of mRNA expression patterns in 3D.