Low Gene Copy Number Research Articles

Effect of Aerobic Exercise in Chinese Adult Individuals at Risk for Type 2 Diabetes Mellitus (T2DM) with Low Salivary Amylase Gene (AMY1) Copy Number Variation.

Type 2 Diabetes mellitus (T2DM) has become a life-threatening health problem around the world. Studies have confirmed that aerobic exercise can prevent the risk of T2DM. Furthermore, recent research showed that salivary amylase gene (AMY1) copy number variation (CNV) could be one of the genetic factors that increased the risk of T2DM. To provide more evidence on how AMY1 CNV and exercise is correlated with the risk of T2DM, we designed this study to show the differences in postprandial carbohydrate metabolism between people with different AMY1 copy numbers, and how aerobic exercise can influence this process. Sixteen participants without cardiovascular disease were chosen, 8 with AMY1 CNV≥6 (High CNV group, HCNV), and 8 with AMY1 CNV ≤ 2 (Low CNV group, LCNV). All participants were Chinese, Han nationality, 18 to 40 years old, with fasting blood glucose lower than 6.1 mmol/L and normal blood pressure levels. They were asked to visit the laboratory in fasting state and drink a cup of solution with 75 grams of edible carbohydrate (glucose or starch). After carbohydrate intake, blood samples were taken at certain times at rest or after aerobic exercise. Blood glucose levels were tested with a portable blood glucose monitor, and insulin levels were tested with the enzyme-linked immunosorbent assay (ELISA). The LCNV group had significantly higher resting insulin levels and homeostatic model assessment of insulin resistance (HOMA-IR) than the HCNV group. Compared to the HCNV group, postprandial blood glucose levels and insulin levels were insensitive to starch intake in the LCNV group. However, this difference disappeared after aerobic exercise was added as an intervention. Lower AMY1 CNV could be associated with higher risk of T2DM and complex carbohydrate metabolism disorder, while aerobic exercise can reduce the risk by increasing the carbohydrate utilization rate.

130 Low Gene Copy Numbers (GCN) of complement C4 and C4A deficiency are highly significant genetic risk factors for idiopathic inflammatory myopathies and its major subgroups

130 Low Gene Copy Numbers (GCN) of complement C4 and C4A deficiency are highly significant genetic risk factors for idiopathic inflammatory myopathies and its major subgroups

Abstract CT214: Preliminary efficacy of telisotuzumab vedotin (Teliso-V) treatment in the 2L/3L setting in MET gene amplified (MET Amp), c-Met protein overexpressing (c-Met OE), non-squamous, non-small cell lung cancer (NSQ NSCLC): Retrospective analysis of LUMINOSITY

Abstract Background: Teliso-V is a first-in-class c-Met-directed antibody-drug conjugate comprising the monoclonal antibody telisotuzumab, a cleavable valine-citrulline linker, and the potent microtubule polymerization inhibitor monomethyl auristatin E. In a Phase 2 study (LUMINOSITY, NCT03539536), Teliso-V has shown an acceptable safety profile and encouraging efficacy in c-Met OE NSQ NSCLC. In NSCLC, while c-Met OE is more common than MET Amp, occurring in 25% of patients (pts) versus 1-5%, respectively, ~90% of MET Amp tumors are c-Met OE. We performed a retrospective analysis of LUMINOSITY to characterize the efficacy of Teliso-V in previously treated pts with MET Amp, c-Met OE NSQ NSCLC. Methods: Pts had locally advanced/metastatic NSQ NSCLC, ≤2 prior lines of systemic therapy, ≤1 line of chemotherapy, MET Amp by fluorescence in situ hybridization (FISH), and tumors that were c-Met OE by central immunohistochemistry (IHC). MET Amp was defined as a ratio of ≥1.8 MET gene copy number (GCN) to chromosome 7 (CEP7) CN by FISH with levels of amplification defined as high, ≥5; intermediate (int), >2.2 - <5; or low, ≥1.8 - ≤2.2. MET GCN by FISH was classified as high, ≥10; int, 5 - <10; or low, <5. c-Met OE was defined as ≥25% of tumor cells at 3+ intensity by IHC; patients were classified as MET IHC 3/25 (25 - 49% tumor cells at 3+) or MET IHC 3/50 (≥50% tumor cells at 3+). Teliso-V was dosed at 1.9 mg/kg IV Q2W. Results: As of 27 May 2021, 10 pts with MET Amp were treated with Teliso-V. The median age was 69 (48-75), 9 pts were male, 5 were White, 9 had a history of smoking (current or former), and 9 had an ECOG score of 0-1. The median MET/CEP7 ratio was 3.3 (1.84-12.17) with 4, 1, and 5 pts having high, int, and low levels of amplification, respectively. The median MET GCN was 10.98 (6.95-65.00) with 6, 3, and 1 pts having high, int, and low GCN, respectively. 7 pts were MET IHC 3/50 and 3 were MET IHC 3/25. Pts with MET Amp treated with Teliso-V monotherapy had an ORR of 80% (95% CI [44.4, 97.5]; n=8; all partial response) by independent central review, and a disease control rate of 90%. The median duration of response was 6.9 months. Among the 8 responders, 62.5% (n=5/8) are still event-free and being followed up for disease assessment. Teliso-V monotherapy resulted in median progression-free survival (PFS) of 8.0 months (95% CI [1.3, -]; n=10), compared with 5.7 months (95% CI [2.6, 9.8]) on the last prior line of systemic cancer therapy (n=10). Conclusions: Teliso-V demonstrated a promising ORR in previously treated pts with MET Amp NSQ NSCLC with c-Met OE and improved PFS when compared to last prior systemic cancer therapy. These preliminary data support the ongoing Phase 2 trial of Teliso-V monotherapy in pts with previously untreated MET Amp NSCLC (TeliMET NSCLC-02; NCT05513703), which is currently enrolling. Citation Format: D. Ross Camidge, Jonathan Goldman, Athan Vasilopoulos, Peter Ansell, Summer Xia, Ellen Bolotin, Jim Looman, Christine Ratajczak, Elysa Noon, Shun Lu. Preliminary efficacy of telisotuzumab vedotin (Teliso-V) treatment in the 2L/3L setting in MET gene amplified (MET Amp), c-Met protein overexpressing (c-Met OE), non-squamous, non-small cell lung cancer (NSQ NSCLC): Retrospective analysis of LUMINOSITY [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT214.

Enhanced production of acetyl-CoA-based products via peroxisomal surface display in Saccharomyces cerevisiae

Colocalization of enzymes is a proven approach to increase pathway flux and the synthesis of nonnative products. Here, we develop a method for enzyme colocalization using the yeast peroxisomal membrane as an anchor point. Pathway enzymes were fused to the native Pex15 anchoring motif to enable display on the surface of the peroxisome facing the cytosol. The peroxisome is the sole location of β-oxidation in Saccharomyces cerevisiae, and acetyl-CoA is a by-product that is exported in the form of acetyl-carnitine. To access this untapped acetyl-CoA pool, we surface-anchored the native peroxisomal/mitochondrial enzyme Cat2 to convert acetyl-carnitine to acetyl-CoA directly upon export across the peroxisomal membrane; this increased acetyl-CoA levels 3.7-fold. Subsequent surface attachment of three pathway enzymes - Cat2, a high stability Acc1 (for conversion of acetyl-CoA to malonyl-CoA), and the type III PKS 2-pyrone synthase - demonstrated the success of peroxisomal surface display for both enzyme colocalization and access to acetyl-CoA from exported acetyl-carnitine. Synthesis of the polyketide triacetic acid lactone increased by 21% over cytosolic expression at low gene copy number, and an additional 11-fold (to 766 mg/L) after further optimization. Finally, we explored increasing peroxisomal membrane area through overexpression of the peroxisomal biogenesis protein Pex11. Our findings establish peroxisomal surface display as an efficient strategy for enzyme colocalization and for accessing the peroxisomal acetyl-CoA pool to increase synthesis of acetyl-CoA-based products.

Low copy numbers of complement C4 and C4A deficiency are risk factors for myositis, its subgroups and autoantibodies

BackgroundIdiopathic inflammatory myopathies (IIM) are a group of autoimmune diseases characterised by myositis-related autoantibodies plus infiltration of leucocytes into muscles and/or the skin, leading to the destruction of blood vessels...

Real-time PCR for detection of pistachio in food targeting a low copy number gene marker

Real-time PCR for detection of pistachio in food targeting a low copy number gene marker

Abstract 2278: Expanding cancer therapy options by leveraging synthetic lethal interactions between druggable paralogs

Abstract Synthetic lethal therapies are a promising approach to expand therapeutic options for cancer patients. Since synthetic lethal therapies target tumor cells specifically, they have fewer off-target effects than oncogene targeted approaches. To identify new cancer drug targets, we focused on paralogs, ancestrally-duplicated genes that frequently retain redundant or overlapping functions. To find synthetic lethal human paralogs, we developed paired guide RNAs for Paralog gENetic interaction mapping (pgPEN), a pooled CRISPR-Cas9 single and double knockout approach targeting over 2,000 paralogs. We applied pgPEN to two cancer cell lines and found that 12% of human paralogs exhibit synthetic lethality in at least one context. To our knowledge, pgPEN represents the largest experimental assessment of human paralog synthetic lethality to date. We next identified paralog pairs to prioritize for follow-up study. A key drawback to synthetic lethal therapies is that many genetic interactions are context-dependent. To identify likely penetrant interactions, we compared our data to other published paralog screens and computational predictions of paralog synthetic lethality. We found that over 75% (n=96) of pgPEN hits were predicted to be broadly synthetic lethal, and nearly 10% (n=10) of pairs were synthetic lethal in multiple paralog screens. Finally, we prioritized paralogs targeted by existing small molecule therapies. Of the 122 synthetic lethal pairs identified by pgPEN, 16% (n=20) are currently druggable. We mined drug repurposing data from DepMap to find pairs where a paralog-targeting drug showed a stronger effect in cell lines with low target gene copy number or expression relative to cell lines with normal target gene copy number or expression. These drugs could selectively target cancer cells in cases where one or both paralogs is lost in tumors but retained in normal tissue. We also leveraged The Cancer Genome Atlas tumor sequencing data to find paralog pairs where one member is recurrently lost in cancer. Taken together, these studies identify druggable, highly penetrant synthetic lethal paralog interactions. In combination with tumor sequencing data, we identify high-priority paralog drug targets that can be further tested and translated to the clinic. Paralog synthetic lethal therapies could provide a relatively low-toxicity therapeutic approach to improve the efficacy of cancer treatments and prevent the emergence of acquired resistance. Citation Format: Phoebe C. Parrish, James D. Thomas, Austin M. Gabel, Shriya Kamlapurkar, Robert K. Bradley, Alice H. Berger. Expanding cancer therapy options by leveraging synthetic lethal interactions between druggable paralogs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2278.

Filling the gaps in Leishmania naiffi and Leishmania guyanensis genome plasticity

Insufficient and irregular data reports on Leishmaniasis, issuing from the developing world, have left much to be desired in terms of understanding the molecular signatures producing distinct infectious phenotypes of the disease. Herein, we report on the complete genome sequencing of Leishmania naiffi and Leishmania guyanensis, sampled from patients in regions of Colombia and Venezuela. In this study, the isolates of cutaneous lesions from both species presented limited structural variation at the chromosomal level, low gene copy number variation, and high genetic heterogeneity. We compared these sequences to the reference genomes hitherto related from Brazil and French Guyana. Although of the same species, we note a consequential genomic disparity between the Venezuelan and French Guyanese isolates of L. guyanensis. Although less significant on the global schema of cutaneous and mucosal disease, such genomic studies of L. naiffi and L. guyanensis substantiate the gaps in understanding of the molecular architecture and multivariate clinical pictures of Leishmaniasis, on an international scale.

Multi-omics Analysis of Ferroptosis Regulation Patterns and Characterization of Tumor Microenvironment in Patients with Oral Squamous Cell Carcinoma.

Ferroptosis is a newly recognized mechanism of regulated cell death. It was reported to be highly associated with immune therapy and chemotherapy. However, its mechanism of regulation in the tumor microenvironment (TME) and influence on oral squamous cell carcinoma (OSCC) therapy are unknown. We identified a ferroptosis-specific gene-expression signature, an FPscore, developed by a principal component analysis (PCA) algorithm to evaluate the ferroptosis regulation patterns of individual tumor. Multi-omics analysis of ferroptosis regulation patterns was conducted. Three distinct ferroptosis regulation subtypes, which linked to outcomes and the clinical relevance of each patient, were established. A high FPscore of patients with OSCC was associated with a favorable prognosis, a ferroptosis-related immune-activation phenotype, potential sensitivities to the chemotherapy and immunotherapy. Importantly, a high FPscore correlated with a low gene copy number burden and high immune checkpoint expressions. We validated the prognostic value of the FPscore using independent immunotherapy and pan-cancer cohorts. Comprehensive evaluation of individual tumors with distinct ferroptosis regulation patterns provides new mechanistic insights, which may be clinically relevant for the application of combination therapies in OSCC.

Capmatinib in MET Exon 14–Mutated or MET-Amplified Non–Small-Cell Lung Cancer

BackgroundAmong patients with non–small-cell lung cancer (NSCLC), MET exon 14 skipping mutations occur in 3 to 4% and MET amplifications occur in 1 to 6%. Capmatinib, a selective inhibitor of the MET receptor, has shown activity in cancer models with various types of MET activation.MethodsWe conducted a multiple-cohort, phase 2 study evaluating capmatinib in patients with MET-dysregulated advanced NSCLC. Patients were assigned to cohorts on the basis of previous lines of therapy and MET status (MET exon 14 skipping mutation or MET amplification according to gene copy number in tumor tissue). Patients received capmatinib (400-mg tablet) twice daily. The primary end point was overall response (complete or partial response), and the key secondary end point was response duration; both end points were assessed by an independent review committee whose members were unaware of the cohort assignments.ResultsA total of 364 patients were assigned to the cohorts. Among patients with NSCLC with a MET exon 14 skipping mutation, overall response was observed in 41% (95% confidence interval [CI], 29 to 53) of 69 patients who had received one or two lines of therapy previously and in 68% (95% CI, 48 to 84) of 28 patients who had not received treatment previously; the median duration of response was 9.7 months (95% CI, 5.6 to 13.0) and 12.6 months (95% CI, 5.6 to could not be estimated), respectively. Limited efficacy was observed in previously treated patients with MET amplification who had a gene copy number of less than 10 (overall response in 7 to 12% of patients). Among patients with MET amplification and a gene copy number of 10 or higher, overall response was observed in 29% (95% CI, 19 to 41) of previously treated patients and in 40% (95% CI, 16 to 68) of those who had not received treatment previously. The most frequently reported adverse events were peripheral edema (in 51%) and nausea (in 45%); these events were mostly of grade 1 or 2.ConclusionsCapmatinib showed substantial antitumor activity in patients with advanced NSCLC with a MET exon 14 skipping mutation, particularly in those not treated previously. The efficacy in MET-amplified advanced NSCLC was higher in tumors with a high gene copy number than in those with a low gene copy number. Low-grade peripheral edema and nausea were the main toxic effects. (Funded by Novartis Pharmaceuticals; GEOMETRY mono-1 ClinicalTrials.gov number, NCT02414139.)

Constraints to counting bioluminescence producing cells by a commonly used transgene promoter and its implications for experimental design

It is routine to genetically modify cells to express fluorescent or bioluminescent reporter proteins to enable tracking or quantification of cells in vitro and in vivo. Herein, we characterized the stability of luciferase reporter systems in C4-2B prostate cancer cells in mono-culture and in co-culture with bone marrow-derived mesenchymal stem/stromal cells (BMSC). An assumption made when employing the luciferase reporter is that the luciferase expressing cell number and bioluminescence signal are linearly proportional. We observed instances where luciferase expression was significantly upregulated in C4-2B cell populations when co-cultured with BMSC, resulting in a significant disconnect between bioluminescence signal and cell number. We subsequently characterized luciferase reporter stability in a second C4-2B reporter cell line, and six other cancer cell lines. All but the single C4-2B reporter cell population had stable luciferase reporter expression in mono-culture and BMSC co-culture. Whole-genome sequencing revealed that relative number of luciferase gene insertions per genome in the unstable C4-2B reporter cell population was lesser than stable C4-2B, PC3 and MD-MBA-231 luciferase reporter cell lines. We reasoned that the low luciferase gene copy number and genome insertion locations likely contributed to the reporter gene expression being exquisitely sensitive BMSC paracrine signals. In this study, we show that it is possible to generate a range of stable and reliable luciferase reporter prostate- and breast- cancer cell populations but advise not to assume stability across different culture conditions. Reporter stability should be validated, on a case-by-case basis, for each cell line and culture condition.

2053-P: Low AMY1 Gene Copy Number Is Associated with Increased Childhood Obesity in Alabama

Salivary amylase (AMY1) is the most abundant enzyme in human saliva, responsible for the hydrolysis of α-1,4 glycosidic linkages that aids in the digestion of dietary starch. Recently few studies have shown that copy number of AMY1 is associated with obesity, however, the data varies with different location. One-third of children are overweight/obese in Alabama. In this study, we specifically aim to determine the relationship between the copy number of AMY1 gene and obesity measurements in elementary school children from Alabama. Sixty elementary school children (30 normal weight and 30 overweight/obese) aged between 6 to 10 years participated in this study. Anthropometric measurements were measured using WHO recommendations. Saliva was collected, genomic DNA was extracted and the copy number of the AMY1 gene was estimated by digital PCR. Linear regression analysis was used to investigate the association between AMY1 copy number and obesity measurements. The mean AMY1 copy number was found to be significantly decreased in obese compared to normal weight children. The results showed a significant inverse association between obesity measurements and AMY1 copy number. Gender-specific analysis showed boys had a stronger association between low AMY1 copy number and obesity compared to girls. Our findings suggest that low AMY1 copy number plays a major role in childhood obesity in Alabama elementary school children and the effect is more prominent in boys compared to girls. Disclosure C. Kurapaty Venkatapoorna: None. P. Ayine: None. E.P. Parra: None. T. Koenigs: None. M. Sandey: None. R.B. Jeganathan: None. G. Thangiah: None. Funding National Institute of Food and Agriculture

Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane

BackgroundFor over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the ‘Saccharum Complex’, an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae.ResultsEight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented.ConclusionFor the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are 8 million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the ‘Saccharum complex’ to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae.

No Impact of Increased EPSPS Gene Copy Number on Growth and Fecundity of Glyphosate-Resistant Kochia (Bassia scoparia)

AbstractThe level of glyphosate resistance in kochia [Bassia scoparia(L.) A. J. Scott] was reported to be due to an increase in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene copy number. A field study was conducted near Manhattan, KS, in 2014 and 2015 to evaluate the relationship between EPSPS gene copy number and growth and fecundity variables ofB. scopariaindividuals within suspected glyphosate-resistant (GR) populations from western Kansas. Initial assays of EPSPS gene copy and in vivo shikimate accumulation showed thatB. scopariapopulations from Finney (FN-R), Scott (SC-R), and Thomas (TH-R) counties were segregating for glyphosate resistance, with some individuals still being glyphosate susceptible (GS). A target-neighborhood competition approach was used to evaluate the competitive response of individual target plants with relatively low (classified as GS) and high (classified as GR) EPSPS gene copy number within the populations. There was no relationship observed between EPSPS gene copy number and vegetative or fecundity variables. There was no differential competitive response of target plant biomass to increasing neighbor density between individuals with low and high EPSPS gene copy number within each population. Lack of associated vegetative growth and fecundity cost to the increased EPSPS gene copy in the GRB. scopariaplants suggests that the plants are likely to persist in field populations, except when effective weed management strategies are adopted that would prevent their growth and seed production.

Low Salivary Amylase Gene (AMY1) Copy Number Is Associated with Obesity and Gut Prevotella Abundance in Mexican Children and Adults.

Genome-wide association studies (GWAS) have identified copy number variants (CNVs) associated with obesity in chromosomal regions 1p31.1, 10q11.22, 11q11, 16p12.3, and recently 1p21.1, which contains the salivary amylase gene (AMY1). Recent evidence suggests this enzyme may influence gut microbiota composition through carbohydrate (mainly starch) degradation. The role of these CNVs in obesity has been scarcely explored in the Latino population, and thus the aim of our study was to evaluate the association of 1p31.1, 10q11.22, 11q11, 16p12.3 and 1p21.1 CNVs with obesity in 921 Mexican children, to replicate significant associations in 920 Mexican adults, and to analyze the association of AMY1 copy number with gut microbiota in 75 children and 45 adults. Of the five CNVs analyzed, 1q11 CNV was significantly associated with obesity in children, but not in adults. Only AMY1 CNV was significantly associated with obesity in both age groups. Moreover, gut microbiota analyses revealed a positive correlation between AMY1 copy number and Prevotella abundance. This genus has enzymes and gene clusters essential for complex polysaccharide degradation and utilization. To our knowledge, this is the first study to analyze the association of these five CNVs in the Mexican population and to report a correlation between AMY1 CN and gut microbiota in humans.

Low Copy Number of the Salivary Amylase Gene (AMY1) Is Associated with Obesity, Dyslipidemia, and Chronic Low-Grade Inflammation but Not Insulin Sensitivity and Secretion

Low salivary amylase gene (AMY1) copy number variations (CNVs) are associated with low serum amylase concentrations which have been shown to correlate with obesity, metabolic syndrome and predict type 2 diabetes. Recently, AMY1 CNV below 4 has been associated higher risk of obesity. Only one study has shown an association between AMY1 CNV and insulin resistance (HOMA). We assessed the relationship between AMY1 CNVs and adiposity (body mass index and dual X-ray absorptiometry), fasting and 2 hour glucose (75g OGTT), insulin sensitivity (hyperinsulinemic euglycemic clamp) and total, first and second phase insulin secretion (intravenous glucose tolerance test), inflammatory markers and adipokines (multiplex assays, Biolegend, CA) in 58 overweight and obese but otherwise healthy individuals (age 31±9 years, BMI 31±4 kg/m2). Participants were non-smokers and had modest alcohol consumption. The participants were divided into two groups according to a median of 4 AMY1 CNVs. Individuals with less than 4 AMY1 CNVs had higher BMI (33±4 vs. 30±3 kg/m2, p=0.04), fat mass (41±12 vs. 34±8kg, p=0.01), LDL cholesterol (3.3 ± 0.8 vs. 2.8±0.7mmol/l, p= 0.02), plasma interleukin 6 (53±56 vs. 24±22 pg/ml, p= 0.02) and leptin concentrations (0.83±0.56 vs. 0.50±0.46 ng/ml, p=0.02) compared to individuals with more than 4 AMY1 CNVs. There was no relationship between AMY1 CNVs and insulin sensitivity, insulin secretion, plasma fasting and 2 hour glucose, high sensitivity C-reactive protein, adiponectin, resistin and adipsin levels (all p>0.1). Our data indicated that AMY1 CNVs are associated with obesity, dyslipidemia and chronic low-grade inflammation but not glucose metabolism. Further larger studies are needed to confirm whether AMY1 CNVs could be a genetic biomarker for metabolic syndrome and type 2 diabetes. Disclosure B. de Courten: None. N. Naderpoor: None.

Impact of TGEV infection on the pig small intestine

BackgroundPig diarrhea causes high mortality and large economic losses in the swine industry. Transmissible gastroenteritis virus (TGEV) causes pig diarrhea, with 100% mortality in piglets less than 2 weeks old. No investigation has yet been made of the small intestine of piglets that survived infection by TGEV.MethodsIn this study, we evaluated the impact of TGEV infection on the small intestine of recovered pigs.ResultsHistological analyses showed that TGEV infection led to villi atrophy, and reduced villous height and crypt depth. The number of SIgA positive cells, CD3+T cells, and dendritic cells (DCs) in jejunum decreased after TGEV infection in vivo. In contrast, microfold cell (M cell) numbers and cell proliferation increased in infected pigs. TGEV infection also significantly enhanced the mRNA expression levels of cytokine IL-1β, IL-6, TNF-α, IL-10, and TGF-β. Additionally, lower gene copy numbers of Lactobacillus, and higher numbers of Enterobacteriaceae, were detected in mucosal scraping samples from TGEV-infected pigs.ConclusionsTGEV infection damages the small intestine, impairs immune functions, and increases pathogenic bacterial loading, all of which may facilitate secondary infections by other pathogens. These findings help quantify the impact of TGEV infection and clarify the pathogenic mechanisms underlying its effects in pigs.

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies

In the past few years, many studies investigated the anaerobic digestion microbiome by means of 16S rRNA amplicon sequencing. Results obtained from these studies were compared to each other without taking into consideration the followed procedure for amplicons preparation and data analysis. This negligence was mainly due to the lack of knowledge regarding the biases influencing specific steps of the microbiome investigation process. In the present study, the main technical aspects of the 16S rRNA analysis were checked giving special attention to the approach used for high throughput sequencing. More specifically, the microbial compositions of three laboratory scale biogas reactors were analyzed before and after addition of sodium oleate by sequencing the microbiome with three different approaches: 16S rRNA amplicon sequencing, shotgun DNA and shotgun RNA. This comparative analysis revealed that, in amplicon sequencing, abundance of some taxa (Euryarchaeota and Spirochaetes) was biased by the inefficiency of universal primers to hybridize all the templates. Reliability of the results obtained was also influenced by the number of hypervariable regions under investigation. Finally, amplicon sequencing and shotgun DNA underestimated the Methanoculleus genus, probably due to the low 16S rRNA gene copy number encoded in this taxon.

Comprehensive approach to study complement C4 in systemic lupus erythematosus: Gene polymorphisms, protein levels and functional activity

Genetic variation of the genes encoding complement component C4 is strongly associated with systemic lupus erythematosus (SLE), a chronic multi-organ auto-immune disease. This study examined C4 and its isotypes on a genetic, protein, and functional level in 140 SLE patients and 104 healthy controls. Gene copy number (GCN) variation, silencing CT-insertion, and the retroviral HERV-K(C4) insertion) were analyzed with multiplex ligation-dependent probe amplification. Increased susceptibility to SLE was found for low GCN (≪2) of C4A. Serositis was the only clinical manifestation associated with low C4A GCN. One additional novel silencing mutation in the C4A gene was found by Sanger sequencing. This mutation causes a premature stop codon in exon 11. Protein concentrations of C4 isoforms C4A and C4B were determined with ELISA and were significantly lower in SLE patients compared to healthy controls. To study C4 isotypes on a functional level, a new C4 assay was developed, which distinguishes C4A from C4B by its binding capacity to amino or hydroxyl groups, respectively. This assay showed high correlation with ELISA and detected crossing over of Rodgers and Chido antigens in 3.2% (8/244) of individuals. The binding capacity of available C4 to its substrates was unaffected in SLE. Our study provides, for the first time, a complete overview of C4 in SLE from genetic variation to binding capacity using a novel test. As this test detects crossing over of Rodgers and Chido antigens, it will allow for more accurate measurement of C4 in future studies.

Expression of the enzymatically active legumain-like cysteine proteinase TvLEGU-1 of Trichomonas vaginalis in Pichia pastoris

The legumain-like cysteine proteinase TvLEGU-1 from Trichomonas vaginalis plays a major role in trichomonal cytoadherence. However, its structure-function characterization has been limited by the lack of a reliable recombinant expression platform to produce this protein in its native folded conformation. TvLEGU-1 has been expressed in Escherichia coli as inclusion bodies and all efforts to refold it have failed. Here, we describe the expression of the synthetic codon-optimized tvlegu-1 (tvlegu-1-opt) gene in Pichia pastoris strain X-33 (Mut+) under the inducible AOX1 promoter. The active TvLEGU-1 recombinant protein (rTvLEGU-1) was secreted into the medium when tvlegu-1-opt was fused to the Aspergillus niger alpha-amylase signal peptide. The rTvLEGU-1 secretion was influenced by the gene copy number and induction temperature. Data indicate that increasing tvlegu-1-opt gene copy number was detrimental for heterologous expression of the enzymatically active TvLEGU-1. Indeed, expression of TvLEGU-1 had a greater impact on cell viability for those clones with 26 or 29 gene copy number, and cell lysis was observed when the induction was carried out at 30 °C. The enzyme activity in the medium was higher when the induction was carried out at 16 °C and in P. pastoris clones with lower gene copy number. The results presented here suggest that both copy number and induction temperature affect the rTvLEGU-1 expression in its native-like and active conformation.