A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

BACKGROUND

Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance.

RESULTS

In reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5-100× more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels.

CONCLUSION

These new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.

The Uncommon Trapezium Fracture: A Case Series

Background  Isolated trapezium fractures are rare and account for only 1 to 5% of all carpal fractures but are still the third most common carpal fracture. Trapezium fractures are hard to detect and easily missed on standard radiographs. Trapezium fractures can be treated conservatively, as well as operatively, the best treatment is still debatable. Damage of the joint surface between the trapezium and the base of the first metacarpal or scaphoid could cause pain and restriction of movements. Therefore, it is important to diagnose and treat the fracture at early stage, so that articular congruence is guaranteed. Case description  We present four cases of the uncommon trapezium fracture. All four cases are conservatively treated with good results, there was no need for operative treatment in all the cases. Literature review  The literature describes the possibility to use fixation techniques, only when it is not possible to reduce the displaced fracture or the residual articular step-off is too high a fixation technique should be used. Clinical relevance  Primarily, we would recommend navicular cast immobilization for 4 to 6 weeks as initial treatment.

Abstract 745: Development of a comprehensive gene fusion NGS panel using an integrated microfluidic circuit enabling highly efficient, multiplex PCR enrichment

Introduction: RNA fusion transcripts result from genomic rearrangements where two distinct genes become juxtaposed and fused. Fusion transcripts are an important class of somatic alterations because they have the potential to create chimeric proteins with altered function, contributing to oncogene activation. These aberrant proteins are expressed in a tumor-specific manner and are thus excellent targets for therapeutic intervention. We have designed an amplicon-based library preparation (LP) kit that targets over 350 fusion gene pairs, representing over 1,000 unique fusion breakpoint events from both solid tumor and hematologic cancers. This panel is specifically designed to run on a newly developed microfluidic integrated fluidic circuit (IFC) that supports flexible amplicon library preparation of 1-6 unique LP panels on a single IFC. Samples can be run against the LP panels in groups of 8, allowing for up to 48 samples per IFC. In this poster we present the results of our analytical validation tests, demonstrating the performance of our comprehensive gene fusion panel on synthetic targets, reference FFPE samples, and subject FFPE samples for use in research studies.

Methods: Primers for amplicon library generation targeting known fusion breakpoints were designed in collaboration with Q2 Solutions®. The panel is comprised of over 1,000 amplicons with an average insert size of 170 bp. Primers were divided into 8 assay pools using informatic parameters that minimize generation of off-target products. Assay pools and cDNA from an off-IFC reverse transcription reaction, along with sample barcodes, were dispensed into designated inlets on an IFC and placed in a Juno™ targeted DNA sequencing library preparation system for mixing the nanoscale reactions, thermal cycling, and amplicon harvesting. Harvested amplicons were collected from the IFC, pooled, and prepared for sequencing on an Illumina® NextSeq™.

Results: The panel was tested against synthetic targets representing all targeted amplicons to demonstrate that each assay reliably detects the intended target of interest. Reference standards and subject FFPE samples were used to assess performance, including positive predictive agreement (PPA), positive predictive value (PPV), and limit of detection. Using these samples at inputs as low as 10 ng of total RNA, PPA and PPV were greater than 99% for the fusion events tested. In addition, fusion events could be reliably detected with as little as 250 copies of target fusion material loaded onto the IFC.

Conclusions: A comprehensive fusion gene panel for targeted next-generation sequencing has been developed using nanoliter-scale PCR based enrichment on a newly developed IFC. Generation of high-quality libraries from a minimum of 10 ng total RNA from FFPE samples for use in research studies has been demonstrated.

Citation Format: Michael L. Gonzales, Jian Qin, Xiaohui Wang, Sangpen Chamnongpol, Jeff Jasper, Thomas Goralski, Christopher Kubu. Development of a comprehensive gene fusion NGS panel using an integrated microfluidic circuit enabling highly efficient, multiplex PCR enrichment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 745.

Abstract 2296: STAR-SEQR: Accurate fusion detection and support for fusion neoantigen applications

Genomic structural variation and associated RNA fusions are a common clinical feature known to be involved in the initiation and pathogenesis of cancer. This complex class of variants also has significant implications on therapeutic decisions and has emerging roles in evidence-based clinical applications. Consequently, fusion detection is an emerging aspect of precision medicine that enables clinical utility of fusions as a therapeutically-relevant target which includes small molecules, biologics, and neoantigen-directed approaches.Here we present STAR-SEQR, an algorithm that uses multiple levels of evidence to detect and quantify fusions from RNA-Seq data. STAR-SEQR is a fast and accurate tool that goes beyond fusion detection and also provides rich annotation and useful reporting features to aid in the adoption of fusions in clinical diagnostics. Notably the software produces fusion expression values, PCR primers, fusion RNA sequence, and predicted peptide sequence to facilitate downstream applications.To address the analytical performance of STAR-SEQR to existing tools, we utilized previously characterized synthetic datasets and real-world sample data with matching DNA sequencing. Of note, in a dataset of 50 synthetic fusions, STAR-SEQR had the highest accuracy of all tools tested and called 49/50 events with no false positives. STAR-SEQR has also been run on several large clinical datasets and the fusion events identified have displayed strong overlap with identified DNA structural variants. STAR-SEQR also performed well in the ongoing ICGC-TCGA DREAM SMC-RNA Challenge and achieved the highest F1 score in the simulated data round with an overall average of 0.96. Analytical lab testing has also been performed using the Seracare Fusion RNA Mix V2 sample containing 15 clinically significant fusions with known concentrations in the low range of detectability. STAR-SEQR accurately called 13/15 events with the other events having no identifiable read alignments. We have also benchmarked methods comparing FFPE material, range of read lengths, and library methods where STAR-SEQR demonstrated excellent tradeoff between sensitivity and precision and generally outperformed other tools.In summary, STAR-SEQR has excellent analytical performance that surpasses existing fusion detection tools. It is broadly applicable to RNA-Seq methods, computationally efficient, and robust across sample characteristics. Lastly, STAR-SEQR is explicitly designed to enable fusion-directed clinical diagnostics and support cancer immunotherapy approaches that utilize fusion neoantigens.

Citation Format: Jeff Jasper, Jason G. Powers, Victor J. Weigman. STAR-SEQR: Accurate fusion detection and support for fusion neoantigen applications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2296.

MiR-148a functions to suppress metastasis and serves as a prognostic indicator in triple-negative breast cancer

Triple-negative breast cancer (TNBC) presents a major challenge in the clinic due to its lack of reliable prognostic markers and targeted therapies. Accumulating evidence strongly supports the notion that microRNAs (miRNAs) are involved in tumorigenesis and could serve as biomarkers for diagnostic purposes. To identify miRNAs that functionally suppress metastasis of TNBC, we employed a concerted approach with selecting miRNAs that display differential expression profiles from bioinformatic analyses of breast cancer patient databases and validating top candidates with functional assays using breast cancer cell lines and mouse models. We have found that miR-148a exhibits properties as a tumor suppressor as its expression is inversely correlated with the ability of both human and mouse breast cancer cells to colonize the lung in mouse xenograft tumor models. Mechanistically, miR-148a appears to suppress the extravasation process of cancer cells, likely by targeting two genes WNT1 and NRP1 in a cell non-autonomous manner. Importantly, lower expression of miR-148a is detected in higher-grade tumor samples and correlated with increased likelihood to develop metastases and poor prognosis in subsets of breast cancer patients, particularly those with TNBC. Thus, miR-148a is functionally defined as a suppressor of breast cancer metastasis and may serve as a prognostic biomarker for this disease.

Abstract 5276: Impact of duplicate removal on low frequency NGS somatic variant calling

Cancer genomic profiles created by analysis of targeted Next Generation Sequencing (NGS) panels is emerging as a powerful tool for making informed clinical decisions. Of the critical informatics challenges to address, accurate mutation calls and allele frequency estimations after accounting for PCR-mediated artifacts are debated. The process of sample preparation for NGS sequencing involves amplification by PCR. While PCR is relatively error-free, mistakes early in DNA synthesis can be compounded, driving detection of spurious mutations and having an adverse impact on clinical reporting. Previous reports have addressed the utility of detecting and removing PCR duplicate reads in Mendelian applications but have rarely examined its use with targeted NGS panels.

We performed deduplication with 3 widely used tools (Samtools, Samblaster, and Picard) to understand sensitivity to call low frequency alleles and any impact on false positive/negative rates. Furthermore, we evaluated effects of duplicate removal on targeted panels of varying sizes and effects of sample matrices using replicates of 7 verified reference samples with several digitally confirmed alleles with frequencies ranging from 1-5%.

It is not practical to perform deduplication on PCR-enriched panels, therefore, we assessed 3 different hybrid enrichment panels of varying size (387kb, 1.3Mb, and 54Mb). Deduplication by Picard resulted in a greater decrease in the mean depth for the smaller panels (32-59%) compared to Exome (15%), showing that higher molecular diversity lowers duplication rates. Uniformity (percent of ROI with depth within 20% of the mean depth) improved 6-18% after deduplication for the smaller panels, but only 1% for the Exome.

Independent of panel size, about 32% of the total reads were marked as duplicates, reducing the power to call low frequency variants by 18%. Importantly, after added sequencing 95-96% of onco-specific variants were detected post-deduplication with a lower limit of detection of 3% compared to 2.5% pre-removal. For low-quality DNA samples we find no benefit in added sequencing for any panel. We also generally observed higher sensitivity (0% to 10% for SNV and -3% to 3% for indels) post deduplication.

Molecular diversity also varies by sample type. Intact DNA show higher molecular diversity and lower duplication rates than degraded FFPE samples. We profiled mixed-quality FFPE samples (n = 85), good-quality fresh frozen samples (n = 3), and NA12878 (n = 1) on our smallest panel and noted duplication rates of 64±14%, 40±5% and 30% respectively. On average, deduplication cut the number of SNV calls by 17.4%, with the FFPE samples affected the most (2-88%).

From our analysis we recommend performing deduplication during analysis of targeted panels. While we observed the most benefit for smaller panels with low uniformity, improved variant sensitivity was seen regardless of panel size. During experimental design, we advise a worksheet to guide deduplication decisions.

Citation Format: Jeran Stratford, Gunjan Hariani, Jeff Jasper, Chad Brown, Wendell Jones, Victor J. Weigman. Impact of duplicate removal on low frequency NGS somatic variant calling. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5276.

Abstract 412: RNA-Seq provides cost-effective alternative for typing self-identifying antigens in immunotherapy patients

The excitement surrounding immunotherapy is being driven by results in the clinic. Currently, autoimmunity is an unfortunate side-effect for a large fraction of those treated. Consequently, understanding how self-antigens are recognized is nearly as important as characterizing the immune repertoire for efficacious delivery of these promising new therapies. One approach to measuring the tumor immune environment is with RNA-Seq assays. Here we show that the genes responsible for presenting self-antigens (HLA Class I and Class II) can also be ascertained from RNA-Seq on total RNA. We present the detailed results from standard RNA-Seq pipeline analysis for 40 lymphoblastoid cell lines to achieve 91.3% overall concordance with “gold standard” typings. These samples were sequenced with 50bp paired-ends and approximately 30M reads. We additionally present RNA-Seq analysis results from calling HLA alleles on 15 replicate pairs of FFPE hepatic tumor samples, finding 88.33% overall replicate concordance with 2-digit precision, and 90% for Class I alleles. Finally, we present HLA-types on triplicates from 2 common breast cancer cell lines, MCF7 and T47D for loci HLA-A,-B,-C,-DRB1,-DQB1, with 90% overall replicate concordance. Emerging targeted DNA-Seq assays aimed at high-throughput clinical trials require high quality whole-blood samples that yield larger amounts of assay input material. Alternatively, the analyses presented here do not require HLA-region enrichment and thus can also be performed on legacy RNA-Seq data. Notably, the data here are generated from sample types and amounts that are more typical to a clinical oncology setting, and because it does not rely on targeted capture as do DNA-Seq assays, these analyses hold greater promise for assembling rare alleles and fusions.

Citation Format: Kimberly Robasky, Jason Powers, Donald Trapolsi, Jeff Jasper, Chad Brown. RNA-Seq provides cost-effective alternative for typing self-identifying antigens in immunotherapy patients. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 412.

Abstract PR11: Dysregulation of cholesterol homeostasis through loss of CYP27A1 in prostate cancer; Implications for early detection and prevention of over-treatment

Approximately 200,000 men are annually diagnosed with prostate cancer (PC), making PC the most commonly diagnosed malignancy among men in industrialized countries. On the other hand, only 30,000 men diagnosed with PC will succumb to the disease with the majority of patients dying from other causes. This makes identification of aggressive vs. indolent PCs one of the most important clinical conundrums in the modern health era. Indeed, identification of biomarkers that achieve this distinction would add a huge benefit and would help patients that have indolent disease avoid side effects associated with treatment modalities that should only be provided to patients with aggressive forms of PC. To achieve the above goal, we employed a bioinformatics based search to look for genes that dramatically change in PC relative to benign and can predict progression. Our mined data from eight different publically available clinical datasets clearly indicates that CYP27A1transcript levels (our top candidate) are down-regulated in PC relative to benign and are further downregulated during PC progression. Our bioinformatics data also shows that patients whose tumors express higher levels of CYP27A1 have longer cancer-free survival following local treatment with radical prostatectomy. To validate these findings, we analyzed expression levels of CYP27A1 protein in benign and cancerous prostate tissue microarrays and found that while 90% of benign prostate cores express CYP27A1, 78% of cancerous cores show low to undetectable expression levels. Given the high rate of CYP27A1 loss in PC, we investigated potential mechanisms using data extracted from The Cancer Genome Atlas (TCGA). We found a very strong inverse and nearly linear relationship between levels of CYP27A1 expression and degree of its promoter methylation (R2=0.79). Conversely, the rate of genetic alterations (mutation, deletion) that might explain loss of CYP27A1expression is very low (3%). Taken together, these results indicate that CYP27A1 loss is an epigenetic event caused by promoter hypermethylation. To investigate the role of CYP27A1 in PC, we reintroduced CYP27A1 in LNCaP and 22Rv1 PC cell lines that have silenced its expression via promoter methylation. Overexpressing CYP27A1 in LNCaP cells significantly retards proliferation in vitro and also slows growth of 22Rv1 subcutaneous xenograft tumors. Given that a major function of CYP27A1 is to convert cholesterol into 27hydroxycholesterol (27HC), we treated five different PC cell lines with 27HC and found that 27HC inhibits PC cells viability in vitro in all cell lines and induces cleavage of PARP, a cellular marker for apoptosis. Finally, we found that 27HC treatment reduces cholesterol levels in PC cells and supplementing PC cells with an exogenous source of cholesterol rescues the cells from 27HC mediated effects. Collectively, our results suggest that 27HC may act as an intracellular cholesterol biosensor and PC cells have developed mechanisms to accumulate more cholesterol through silencing of CYP27A1 and stopping the production of 27HC. This is key, as epidemiological and experimental evidence strongly suggests that hypercholesterolemia is associated with an increased risk of lethal PC. Our results highlight CYP27A1 loss as a promising biomarker for PC and also suggest that reduction of intratumoral cholesterol may have a preventative role in PC possibly through treatment with 27HC.

Citation Format: Mahmoud A. Alfaqih, Erik R. Nelson, Rachid Safi, Jeff Jasper, Donald P. McDonnell, Stephen J. Freedland. Dysregulation of cholesterol homeostasis through loss of CYP27A1 in prostate cancer; Implications for early detection and prevention of over-treatment. [abstract]. In: Proceedings of the Thirteenth Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2014 Sep 27-Oct 1; New Orleans, LA. Philadelphia (PA): AACR; Can Prev Res 2015;8(10 Suppl): Abstract nr PR11.

Effect of aerobic training on the host systemic milieu in patients with solid tumours: an exploratory correlative study

Background:

Few studies have investigated the effects of exercise on modulation of host factors in cancer patients. We investigated the efficacy of chronic aerobic training on multiple host-related effector pathways in patients with solid tumours.

Patients and Methods:

Paired peripheral blood samples were obtained from 44 patients with solid tumours receiving cytotoxic therapy and synthetic erythropoietin (usual care; n=21) or usual care plus supervised aerobic training (n=23) for 12 weeks. Samples were characterised for changes in immune, cytokine and angiogenic factors, and metabolic intermediates. Aerobic training consisted of three supervised cycle ergometry sessions per week at 60% to 100% of peak oxygen consumption (VO_2peak), 30–45 min per session, for 12 weeks following a nonlinear prescription.

Results:

The between-group delta change in cardiopulmonary function was +4.1 ml kg ⁻¹ min⁻¹, favouring aerobic training (P<0.05). Significant pre–post between-group differences for five cytokine and angiogenic factors (HGF, IL-4, macrophage inflammatory protein-1β (MIP-1β), vascular endothelial growth factor (VEGF), and TNF-α) also favour the aerobic training group (P's<0.05). These reductions occurred in conjunction with nonsignificant group differences for T lymphocytes CD4⁺, CD8⁺, and CD8⁺/CD45RA (P<0.10). For these factors, circulating concentrations generally increased from baseline to week 12 in the aerobic training group compared with decreases or no change in the usual care group. No significant changes in any metabolic intermediates were observed.

Conclusions:

Aerobic training alters host availability of select immune–inflammatory effectors in patients with solid tumours; larger confirmatory studies in more homogenous samples are warranted.

Abstract 3311: The cholesterol/ 27-hydroxycholesterol axis is a novel therapeutic target in castrate resistant prostate cancer

The most recent estimates indicate that men have a seventeen percent chance of developing invasive prostate cancer (PCa) over their lifetime. This makes PCa the most commonly diagnosed malignancy among men in industrialized countries, accounting for the second leading cause of cancer-related deaths. Although PCa almost always develops resistance to androgen-deprivation therapy, both androgen receptor (AR) itself and the processes downstream of the receptor remain active and are necessary for cancer progression and thus continue to be viable targets for therapeutic intervention. In this regard, it is of significance that several independent studies demonstrate a link between elevated intra-prostatic levels of cholesterol and the presence of malignancy. This puts into context our current finding that 27-hydroxycholesterol (27HC), a primary metabolite of cholesterol, regulates pathways and processes that oppose AR action. For example, AR activation results in a net uptake of cholesterol by PCa cells and enhances denovo lipogenesis, while 27HC down-regulates genes involved in cholesterol uptake and activates those involved in its efflux. More importantly, we show that treatment of PCa cell lines with 27HC inhibits their proliferation, an activity that is reversed upon supplementing the cells with an exogenous source of cholesterol or upon over-expression of low density lipoprotein receptor (LDLR), a membrane protein that mediates the uptake of cholesterol. In prostatic tissues, 27HC is synthesized directly from cholesterol by the cytochrome P450 enzyme, CYP27A1. To further highlight the above axis as a novel therapeutic target, using data mining approaches from clinical databases, we show that (1) transcript levels of CYP27A1 are dramatically down-regulated during PCa progression and (2) patients whose tumors express high levels of CYP27A1transcript exhibit longer disease free survival. Most notably, we were able to show that over-expression of CYP27A1 inhibits the proliferation of PCa cell lines in vitro and delays the growth of xenografts in castrated immune-deficient mice. In summary, our data thus far strongly implicates that CYP27A1 is a potential tumor suppressor in PCa and highlights the cholesterol/27HC axis as a target for the development of novel therapeutics for castrate resistant disease.

Citation Format: Mahmoud A. Alfaqih, Erik R. Nelson, Rachid Safi, Jeff Jasper, Ching-yi Chang, Stephen J. Freedland, Donald P. McDonnell. The cholesterol/ 27-hydroxycholesterol axis is a novel therapeutic target in castrate resistant prostate cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3311. doi:10.1158/1538-7445.AM2014-3311

Obesity, cholesterol metabolism, and breast cancer pathogenesis

Obesity and altered lipid metabolism are risk factors for breast cancer in pre- and post-menopausal women. These pathologic relationships have been attributed in part to the impact of cholesterol on the biophysical properties of cell membranes and to the influence of these changes on signaling events initiated at the membrane. However, more recent studies have indicated that the oxysterol 27-hydroxycholesterol (27HC), and not cholesterol per se, may be the primary biochemical link between lipid metabolism and cancer. The enzyme responsible for production of 27HC from cholesterol, CYP27A1, is expressed primarily in the liver and in macrophages. In addition, significantly elevated expression of this enzyme within breast tumors has also been observed. It is believed that 27HC, acting through the liver X receptor in macrophages and possibly other cells, is involved in maintaining organismal cholesterol homeostasis. It has also been shown recently that 27HC is an estrogen receptor agonist in breast cancer cells and that it stimulates the growth and metastasis of tumors in several models of breast cancer. These findings provide the rationale for the clinical evaluation of pharmaceutical approaches that interfere with cholesterol/27HC synthesis as a means to mitigate the impact of cholesterol on breast cancer pathogenesis. Cancer Res; 74(18); 4976-82. ©2014 AACR.

Effects of ad libitum milk intake on dairy calves

Conventional milk feeding for calves (by bucket twice daily at a total of 10% of body weight) was compared with feeding milk for ad libitum consumption from a nipple. Calves were weaned gradually between d 37 and 42 by diluting the milk with water, and body weight and feed consumption were followed until d 63. Calves fed ad libitum drank 89% more milk than calves fed conventionally during the preweaning period, but the ad libitum-fed calves ate only 16% as much calf starter and 17% as much hay. Consumption of starter and hay increased rapidly after weaning, and treatment differences disappeared. Probably as a result of the much higher intake of milk, the ad libitum-fed calves gained 63% more weight than the conventionally fed calves before weaning, resulting in a 10.5-kg weight advantage on d 35. During and immediately after weaning, the rate of weight gain slowed for both treatment groups, but recovered by approximaely d 49. There were no treatment differences in weight gains over the weaning or postweaning periods, and at the end of the experiment on d 63, the calves fed ad libitum maintained an advantage in mean (+/- SEM) body weight (89.07 +/- 2.47 kg vs 81.07 +/- 2.47 kg for the conventionally fed calves). Incidence of diarrhea was low and did not differ between treatment groups. We conclude that ad libitum nipple feeding of milk to dairy calves can allow for increased milk intake and weight gain with no detrimental effects on intake of solid food after weaning.

Decreased transcript expression coincident with impaired glycosylation in the beta2-adrenergic receptor gene does not result from differences in the primary sequence

Variants of the S49 mouse lymphoma cell line exhibit multiple lesions along the pathway of cyclic AMP generation in response to beta2-adrenergic stimulation. Two such variants, beta(p) and beta(d), are characterized by decreased receptor binding and mRNA expression, 50% and 25% of wild-type receptor expression, respectively. The rate of beta2-adrenergic receptor synthesis was measured and found to be decreased in the beta d cells vis-a-vis the rate in wild type cells. The molecular mass of the beta2-adrenergic receptor in the S49 wild-type, beta(p) and beta(d) variant cells was estimated by labeling the receptor with the photoaffinity probe [125I]iodocyanopindololdiazirine. Receptor size was found to be 67,000 and 47,000 Da in the wild-type and 60,000 and 42,000 in the two variant cells. This 6 kDa discrepancy in mass was abolished upon treatment of labeled cell extracts with N-glycosidase F, suggesting the possibility of either N-terminal truncation or altered glycosylation of the receptor in the variant cells. To distinguish between these possibilities, we sequenced the beta2-adrenergic receptor gene and two kilobases of the 5'-non-coding region. No differences were found in the coding region of the gene from wild-type, beta(p) and beta(d) S49 cells suggesting that both the diminished expression and the decreased size of beta2-adrenergic receptor in the beta(p) and beta(d) S49 variants are related to impaired glycosylation of the receptor. This hypothesis was substantiated by the reduced retention of the variant cells' beta2-adrenergic receptor on immobilized WGA. Furthermore, growth of the S49 cells in the presence of the alpha-mannosidase II inhibitor, swainsonine, preferentially impaired the ability of the receptors derived from the variant cells to bind to WGA. These results imply that altered expression and glycosylation of G-protein-linked receptors occur as a consequence of one or more mutations outside the receptor's open reading frame.

RS-17053 (N-[2-(2-cyclopropylmethoxyphenoxy)ethyl]-5-chloro-alpha, alpha-dimethyl-1H-indole-3-ethanamine hydrochloride), a selective alpha 1A-adrenoceptor antagonist, displays low affinity for functional alpha 1-adrenoceptors in human prostate: implications for adrenoceptor classification

Norepinephrine (NE) contracts smooth muscle cells within the human lower urinary tract (LUT) (bladder neck, prostate, and urethra). Receptor distribution and pharmacological evidence have implicated activation of alpha 1A-adrenoceptors. We disclose the pharmacological properties of the novel, selective alpha 1A-adrenoceptor antagonist N-[2-(2-cyclopropylmethoxyphenoxy)ethyl]-5-chloro- alpha,alpha-dimethyl-1H-indole-3-ethanamine hydrochloride (RS-17053) and examine critically the pharmacological identity of the alpha 1-adrenoceptor mediating contractions to NE in human LUT tissues. In several tissues from rat and cloned adrenoceptors, RS-17053 displayed high affinity for the alpha 1A-adrenoceptor (pKi and pA2 estimates of 9.1-9.9) and a 30-100-fold selectivity over the alpha 1B- and the alpha 1D-adrenoceptor subtypes (pK1 and pA2 estimates of 7.7-7.8). However, in isolated smooth muscle preparations from human LUT tissues, RS-17053 antagonized responses to NE only at high concentrations. Estimates of affinity (pA2) at alpha 1-adrenoceptors mediating NE-induced contractions were 7.5 in prostatic periurethral longitudinal smooth muscle (compared with 8.6 for prazosin), 6.9 in anterior fibromuscular stroma (prazosin, 8.9), and 7.1 in bladder neck (prazosin, 8.5). These findings indicate that contractile responses to NE in human LUT tissues are mediated by a receptor displaying pharmacological properties that are clearly different from those of the defined alpha 1A-adrenoceptor and raise the possibility that multiple forms of the alpha 1A-adrenoceptor may exist in human LUT that are discriminated by RS-17053. In this regard, the affinity estimates obtained with RS-17053 and other alpha 1-adrenoceptor antagonists in human LUT tissues are identical to those described for the putative alpha 1L-adrenoceptor.

Developmental expression of connexins in the chick embryo myocardium and other tissues

BACKGROUND

Connexins are cell surface proteins that form specialized regions of cell-cell communication called gap junctions. These allow impulse conduction in in voluntary muscle tissue such as the heart, but also allow the formation of communities of like cells during development of organs.

METHODS

We used an antipeptide antibody to connexin 43 in immunolocalization studies and an anti-peptide antibody to an external loop domain common to most connexins in Western blotting of total heart protein to measure the accumulation of connexins in the heart as it develops from 33 hours to 21 days (hatching), and in the adult.

RESULTS

Immunolocalization revealed that connexin 43 is widely distributed in the earliest organ rudiments. It is especially prominent in the neural tube and its derivatives, in the lens and nasal placodes, in the foregut and its derivatives, in the somites, in the mesonephric tubules, and in the heart and major arteries. Heart tissue staining grew more intense with development through day 8. However, at day 11 and day 15, and in the adult, heart staining diminished. Endocardium and valve tissue did not stain. Western blotting of heart homogenates with the antibody directed against the external loop domain peptide showed 26, 32, 43, 45, and 56 kilodalton connexins, which changed in relative abundance, displaying unique patterns during development.

CONCLUSIONS

Our results show patterns of connexin immunolocalization in early germ layers and organ rudiments that are similar to those known in the mouse, but with certain differences. Our results show a distinctive pattern of multiple connexin gene expression in the developing heart from days 2-21.