A High-Coverage Mesolithic Aurochs Genome and Effective Leveraging of Ancient Cattle Genomes Using Whole Genome Imputation

Ancient genomic analyses are often restricted to utilizing pseudohaploid data due to low genome coverage. Leveraging low-coverage data by imputation to calculate phased diploid genotypes that enables haplotype-based interrogation and single nucleotide polymorphism (SNP) calling at unsequenced positions is highly desirable. This has not been investigated for ancient cattle genomes despite these being compelling subjects for archeological, evolutionary, and economic reasons. Here, we test this approach by sequencing a Mesolithic European aurochs (18.49×; 9,852 to 9,376 calBCE) and an Early Medieval European cow (18.69×; 427 to 580 calCE) and combine these with published individuals: two ancient and three modern. We downsample these genomes (0.25×, 0.5×, 1.0×, and 2.0×) and impute diploid genotypes, utilizing a reference panel of 171 published modern cattle genomes that we curated for 21.7 million (Mn) phased SNPs. We recover high densities of correct calls with an accuracy of >99.1% at variant sites for the lowest downsample depth of 0.25×, increasing to >99.5% for 2.0× (transversions only, minor allele frequency [MAF] ≥ 2.5%). The recovery of SNPs correlates with coverage; on average, 58% of sites are recovered for 0.25× increasing to 87% for 2.0×, utilizing an average of 3.5 million (Mn) transversions (MAF ≥2.5%), even in the aurochs, despite the highest temporal distance from the modern reference panel. Our imputed genomes behave similarly to directly called data in allele frequency-based analyses, for example consistently identifying runs of homozygosity >2 Mb, including a long homozygous region in the Mesolithic European aurochs.

Transcriptomic analysis of intestinal organoids, derived from pigs divergent in feed efficiency, and their response to Escherichia coli

BACKGROUND

There is increasing interest in using intestinal organoids to study complex traits like feed efficiency (FE) and host-microbe interactions. The aim of this study was to investigate differences in the molecular phenotype of organoids derived from pigs divergent for FE as well as their responses to challenge with adherent and invasive Escherichia coli (E. coli).

RESULTS

Colon and ileum tissue from low and high FE pigs was used to generate 3D organoids and two dimensional (2D) monolayers of organoid cells for E. coli challenge. Genome-wide gene expression was used to investigate molecular differences between pigs that were phenotypically divergent for FE and to study the difference in gene expression after challenge with E. coli. We showed, (1) minor differences in gene expression of colon organoids from pigs with low and high FE phenotypes, (2) that an E. coli challenge results in a strong innate immune gene response in both colon and ileum organoids, (3) that the immune response seems to be less pronounced in the colon organoids of high FE pigs and (4) a slightly stronger immune response was observed in ileum than in colon organoids.

CONCLUSIONS

These findings demonstrate the potential for using organoids to gain insights into complex biological mechanisms such as FE.

Peripheral inflammation-induced changes in songbird brain gene expression: 3' mRNA transcriptomic approach

Species-specific neural inflammation can be induced by profound immune signalling from periphery to brain. Recent advances in transcriptomics offer cost-effective approaches to study this regulation. In a population of captive zebra finch (Taeniopygia guttata), we compare the differential gene expression patterns in lipopolysaccharide (LPS)-triggered peripheral inflammation revealed by RNA-seq and QuantSeq. The RNA-seq approach identified more differentially expressed genes but failed to detect any inflammatory markers. In contrast, QuantSeq results identified specific expression changes in the genes regulating inflammation. Next, we adopted QuantSeq to relate peripheral and brain transcriptomes. We identified subtle changes in the brain gene expression during the peripheral inflammation (e.g. up-regulation in AVD-like and ACOD1 expression) and detected co-structure between the peripheral and brain inflammation. Our results suggest benefits of the 3'end transcriptomics for association studies between peripheral and neural inflammation in genetically heterogeneous models and identify potential targets for the future brain research in birds.

A compendium of genetic regulatory effects across pig tissues

The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.

Potential selection for lipid kinase activity and spermatogenesis in Henan native pig breeds and growth shaping by introgression of European genes

BACKGROUND

China has one third of the worldwide indigenous pig breeds. The Henan province is one of the earliest pig domestication centers of China (about 8000 years ago). However, the precise genetic characteristics of the Henan local pig breeds are still obscure. To understand the origin and the effects of selection on these breeds, we performed various analyses on lineage composition, genetic structure, and detection of selection sweeps and introgression in three of these breeds (Queshan, Nanyang and Huainan) using genotyping data on 125 Queshan, 75 Nanyang, 16 Huainan pigs and 878 individuals from 43 Eurasian pig breeds.

RESULTS

We found no clear evidence of ancestral domestic pig DNA lineage in the Henan local breeds, which have an extremely complicated genetic background. Not only do they share genes with some northern Chinese pig breeds, such as Erhualian, Hetaodaer, and Laiwu, but they also have a high admixture of genes from foreign pig breeds (33-40%). Two striking selection sweeps in small regions of chromosomes 2 and 14 common to the Queshan and Nanyang breeds were identified. The most significant enrichment was for lipid kinase activity (GO:0043550) with the genes FII, AMBRA1, and PIK3IP1. Another interesting 636.35-kb region on chromosome 14 contained a cluster of spermatogenesis genes (OSBP2, GAL3ST1, PLA2G3, LIMK2, and PATZ1), a bisexual sterility gene MORC2, and a fat deposition gene SELENOM. Reproduction and growth genes LRP4, FII, and ARHGAP1 were present in a 238.05-kb region on SSC2 under selection. We also identified five loci associated with body length (P = 0.004) on chromosomes 1 and 12 that were introgressed from foreign pig breeds into the Henan breeds. In addition, the Chinese indigenous pig breeds fell into four main types instead of the previously reported six, among which the Eastern type could be divided into two subgroups.

CONCLUSIONS

Admixture of North China, East China and foreign pigs contributed to high genetic diversity of Henan local pigs. Ontology terms associated with lipid kinase activity and spermatogenesis and growth shaping by introgression of European genes in Henan pigs were identified through selective sweep analyses.

Integrative metabolomic and transcriptomic analysis reveals difference in glucose and lipid metabolism in the longissimus muscle of Luchuan and Duroc pigs

Luchuan pig, an obese indigenous Chinese porcine breed, has a desirable meat quality and reproductive capacity. Duroc, a traditional western breed, shows a faster growth rate, high feed efficiency and high lean meat rate. Given the unique features these two porcine breeds have, it is of interest to investigate the underlying molecular mechanisms behind their distinctive nature. In this study, the metabolic and transcriptomic profiles of longissimus dorsi muscle from Duroc and Luchuan pigs were compared. A total of 609 metabolites were identified, 77 of which were significantly decreased in Luchuan compared to Duroc, and 71 of which were significantly elevated. Most differentially accumulated metabolites (DAMs) upregulated in Luchuan were glycerophospholipids, fatty acids, oxidized lipids, alcohols, and amines, while metabolites downregulated in Luchuan were mostly amino acids, organic acids and nucleic acids, bile acids and hormones. From our RNA-sequencing (RNA-seq) data we identified a total of 3638 differentially expressed genes (DEGs), 1802 upregulated and 1836 downregulated in Luchuan skeletal muscle compared to Duroc. Combined multivariate and pathway enrichment analyses of metabolome and transcriptome results revealed that many of the DEGs and DAMs are associated with critical energy metabolic pathways, especially those related to glucose and lipid metabolism. We examined the expression of important DEGs in two pathways, AMP-activated protein kinase (AMPK) signaling pathway and fructose and mannose metabolism, using Real-Time Quantitative Reverse Transcription PCR (qRT-PCR). Genes related to glucose uptake, glycolysis, glycogen synthesis, fatty acid synthesis (PFKFB1, PFKFB4, MPI, TPI1, GYS1, SLC2A4, FASN, IRS1, ULK1) are more activated in Luchuan, while genes related to fatty acid oxidation, cholesterol synthesis (CPT1A, HMGCR, FOXO3) are more suppressed. Energy utilization can be a decisive factor to the distinctive metabolic, physiological and nutritional characteristics in skeletal muscle of the two breeds we studied. Our research may facilitate future porcine breeding projects and can be used to reveal the potential molecular basis of differences in complex traits between various breeds.

Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines

The pig IPEC-J2 and chicken SL-29 cell lines are of interest because of their untransformed nature and wide use in functional studies. Molecular characterization of these cell lines is important to gain insight into possible molecular aberrations. The aim of this paper is to provide a molecular and epigenetic characterization of the IPEC-J2 and SL-29 cell lines, a cell-line reference for the FAANG community, and future biomedical research. Whole genome sequencing, gene expression, DNA methylation, chromatin accessibility, and ChIP-seq of four histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3) and an insulator (CTCF) are used to achieve these aims. Heteroploidy (aneuploidy) of various chromosomes was observed from whole genome sequencing analysis in both cell lines. Furthermore, higher gene expression for genes located on chromosomes with aneuploidy in comparison to diploid chromosomes was observed. Regulatory complexity of gene expression, DNA methylation, and chromatin accessibility was investigated through an integrative approach.

Imputation of Ancient Whole Genome Sus scrofa DNA Introduces Biases Toward Main Population Components in the Reference Panel

Sequencing ancient DNA to high coverage is often limited by sample quality and cost. Imputing missing genotypes can potentially increase information content and quality of ancient data, but requires different computational approaches than modern DNA imputation. Ancient imputation beyond humans has not been investigated. In this study we report results of a systematic evaluation of imputation of three whole genome ancient Sus scrofa samples from the Early and Late Neolithic (∼7,100–4,500 BP), to test the utility of imputation. We show how issues like genetic architecture and, reference panel divergence, composition and size affect imputation accuracy. We evaluate a variety of imputation methods, including Beagle5, GLIMPSE, and Impute5 with varying filters, pipelines, and variant calling methods. We achieved genotype concordance in most cases reaching above 90%; with the highest being 98% with ∼2,000,000 variants recovered using GLIMPSE. Despite this high concordance the sources of diversity present in the genotypes called in the original high coverage genomes were not equally imputed leading to biases in downstream analyses; a trend toward genotypes most common in the reference panel is observed. This demonstrates that the current reference panel does not possess the full diversity needed for accurate imputation of ancient Sus, due to missing variations from Near Eastern and Mesolithic wild boar. Imputation of ancient Sus scrofa holds potential but should be approached with caution due to these biases, and suggests that there is no universal approach for imputation of non-human ancient species.

The Visayan warty pig (Sus cebifrons) genome provides insight into chromosome evolution and sensory adaptation in pigs

It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks post-zygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent post-divergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.

POS0298 OCCURRENCE AND PREDICTION OF FLARE AFTER TAPERING OF TNF INHIBITORS IN PATIENTS WITH AXIAL SPONDYLOARTHRITIS

Background

Patients with axial spondyloarthritis (axSpA) in clinical remission tapered Tumor Necrosis Factor inhibitor (TNFi) therapy according to a clinical guideline and had 2 years´ follow-up [1].

Objectives

We aimed to investigate flare frequency, dose at which flare occurred, type of flare (clinical/ Bath ankylosing spondylitis disease activity index (BASDAI)/magnetic resonance imaging (MRI)) and predictors of flare.

Methods

Patients in clinical remission (BASDAI<40, physician global score<40 and without disease activity the previous year) tapered TNFi to 2/3 standard dose at baseline, 1/2 at week (w)16, 1/3 at w32 and 0 (discontinuation) at w48. Patients who flared were increased to previous dose. Predictors of flare at each dose step were investigated by regression analyses.

Results

Of 108 patients, 106 (99%) flared before year 2 (flare occurring mean (SD) 99(44.3) days after last tapering). Twenty-nine patients (27%) flared at 2/3 standard dose, 21 (20%) at 1/2 dose, 29 (27%) at 1/3 dose and 27 (25%) after discontinuation. One-hundred-and-five (99%) had clinical flare, 25 (24%) BASDAI flare and 23 (29% of patients with MRI at flare) MRI flare; and forty-one patients (41%) fulfilled the ASAS-definition of clinically important worsening (≥0.9 increase since baseline) (Figure 1). Most common flare symptoms were back/buttock pain (n=93 (89%)) and pain in peripheral joints/entheseal regions (n=48 (46%)). Higher baseline physician global score was an independent predictor of flare after tapering to 2/3 (Odds ratio=1.19 (95% Confidence Interval=1.05-1.41); p=0.011) (Table 1). Changes in clinical and/or imaging variables in the 16 weeks prior to tapering did not predict flare (data not shown).

Table 1.

Prediction of flare within 16 weeks after tapering to 2/3 dose (n=74)

Values are from timepoint of tapering from full dose to 2/3 doseUnivariate analysesFinal multivariable analyses*OR(95% CI)p-valueOR(95% CI)p-valueMale gender0.96(0.25 - 4.14)0.955Age1.00(0.96 - 1.04)0.880Time since diagnosis1.00(0.95 - 1.06)0.863Current smoker0.70(0.20 - 2.20)0.543HLA-B27 positive0.66(0.18 - 2.41)0.515Previous bDMARDs1.28(0.66 - 2.49)0.458Patient pain VAS1.02(0.98 - 1.06)0.310Physician global VAS1.19(1.04 - 1.41)0.0121.19(1.04 - 1.41)0.011ASDAS1.66(0.70 - 4.10)0.251mNYc positive0.78(0.29 - 2.09)0.615SPARCC SIJ Inflammation Index1.01(0.90 - 1.12)0.861CANDEN Total inflammation0.95(0.65 - 1.25)0.702SPARCC SSS Erosion1.11(0.91 - 1.37)0.293CANDEN Fat0.99(0.96 - 1.02)0.705AUC (95% CI)0.66 (0.54 - 0.78)

Predictors were selected by applying backward selection in stacked data. p-values by likelihood ratio tests. Bold indicates p-values<0.1 in univariate analyses. Predictors were selected by backward selection in stacked imputed datasets after applying a fixed weight to all observations, accounting for the average fraction of missing data across all variables under consideration. *Results were derived in non-imputed data (no missing values in selected predictors). CIs given as profile likelihood CIs. AUC estimated based on internal validation by bootstrapping with 1000 samples.

ASDAS, Ankylosing Spondylitis Disease Activity Score; bDMARDs, biological disease modifying anti-rheumatic drugs; AUC, Area Under the receiver operating characteristic Curve; CANDEN, Canada-Denmark MRI scoring system of the spine in patients with axial spondyloarthritis; CI, confidence interval; mNYc, modified New York criteria; SIJ, sacroiliac joint; SPARCC SIJ inflammation, Spondyloarthritis Research Consortium of Canada Sacroiliac joint inflammation; SPARCC SSS, Spondyloarthritis Research Consortium of Canada Sacroiliac joint Structural Score; VAS, visual analogue scale.

Conclusion

Almost all (99%) axSpA patients in clinical remission flared during tapering to discontinuation, but above half not before receiving 1/3 dose or less. Higher physician global score was the only independent predictor of flare.

References

[1]Wetterslev M, et al. Rheumatology (Oxford) 2021;10.1093/rheumatology/keab755.

Disclosure of Interests

Marie Wetterslev: None declared, Stylianos Georgiadis: None declared, Sara Nysom Christiansen Speakers bureau: BMS and GE, Grant/research support from: Novartis, Susanne Juhl Pedersen Speakers bureau: MSD, Pfizer, AbbVie, Novartis and UCB, Consultant of: AbbVie and Novartis, Grant/research support from: AbbVie, MSD, and Novartis, Inge Juul Sørensen: None declared, Merete Lund Hetland Consultant of: MSD, Biogen, Pfizer, Eli Lilly, Orion Pharma, CellTrion, Samsung Bioepis, and Janssen Biologics BV, Grant/research support from: MSD, Biogen, Pfizer, Bristol-Myers Squibb, AbbVie, Roche and Novartis, Anne Duer: None declared, Mikael Boesen Speakers bureau: Image Analysis Group, Esaote, AbbVie, Celgene, Eli-Lilly, Janssen, Novartis, Pfizer, UCB, Novo, GSK, Takeda, Geurbet, Biogen, Radiobotics and Chondrometrics, Consultant of: Image Analysis Group, Esaote, AbbVie, Celgene, Eli-Lilly, Janssen, Novartis, Pfizer, UCB, Novo, GSK, Takeda, Geurbet, Biogen, Radiobotics and Chondrometrics, Grant/research support from: Image Analysis Group, Esaote, AbbVie, Celgene, Eli-Lilly, Janssen, Novartis, Pfizer, UCB, Novo, GSK, Takeda, Geurbet, Biogen, Radiobotics and Chondrometrics, Kasper K Gosvig: None declared, Jakob Møllenbach Møller: None declared, Mads Bakkegaard: None declared, Cecilie Heegaard Brahe: None declared, Niels Steen Krogh: None declared, Bente Jensen: None declared, Ole Madsen: None declared, Jan Christensen: None declared, Annette Hansen Speakers bureau: speaker fees from Elly Lilly, Jesper Noerregaard: None declared, Henrik Røgind: None declared, Mikkel Østergaard Speakers bureau: Abbvie, BMS, Boehringer-Ingelheim, Celgene, Eli-Lilly, Hospira, Janssen, Merck, Novartis, Pfizer, Regeneron, Roche, Sandoz, Sanofi and UCB, Consultant of: Abbvie, BMS, Boehringer-Ingelheim, Celgene, Eli-Lilly, Hospira, Janssen, Merck, Novartis, Pfizer, Regeneron, Roche, Sandoz, Sanofi and UCB, Grant/research support from: Abbvie, BMS, Boehringer-Ingelheim, Celgene, Eli-Lilly, Hospira, Janssen, Merck, Novartis, Pfizer, Regeneron, Roche, Sandoz, Sanofi and UCB

AB0801 The ASAS Health Index (HI): Construct validity and responsiveness in relation to TNF inhibitor (TNFi) treatment in patients with axial spondyloarthritis (axSpA)

Background

The Assessment of Spondyloarthritis International Society (ASAS) has developed the ASAS HI aiming to capture the full range of functioning and disability in patients with axSpA.

Objectives

To examine the construct validity and responsiveness of ASAS HI in relation to TNFi treatment.

Methods

In this investigator-initiated 52-week prospective observational study (MANGO study; NCT02011386)(3) axSpA patients initiated sc. Golimumab 50 mg every month. Key inclusion criteria were BASDAI >4.0 and sacroiliitis on radiography and/or MRI.

Results

45 of 53 TNFi naïve patients completed ASAS HI at weeks 0, 4, 16 and 52. 55.6% were male, 75.6% HLA-B27 positive, median age 34.6 yrs (IQR 28.3;46.1) and symptom duration 5.1 yrs. (2;13)(Table 1A). ASAS HI decreased from week 0 to weeks 4, 16 and 52, from median 10.0 (IQR 8;11)) to 7.0 (2.3;10), 5.5 (1.3;8) and 4.0 (1;7.5)(Wilcoxon-Pratt; all p<0.001). Patients with low ASAS HI (score 0-5, good heath state(4)) at week 16 and 52 had significantly lower ASDAS, BASDAI, BASFI, pain, pt. global and CRP than patients with moderate to high ASAS HI (6-17) (Table 1B). Patients with a decrease of >3 (clinically meaningful change(3)) or >30%(5) in ASAS HI from week 0-16 had significantly larger reductions in ASDAS, BASDAI, BASFI, pain, pt. global and SPARCC MRI spine inflammation score (Table 1C). At baseline, ASAS HI correlated with BASFI and SPARCC SIJ inflammation score (rho: 0.37-0.38, p<0.05), and changes in ASAS HI from week 0-16 correlated with changes in ASDAS, BASDAI, BASFI, pain, pt. global (0.51-0.67, p<0.001) and change in MRI SIJ inflammation score (0.30, p<0.05). ASAS HI had high responsiveness (Table 1D).

Table 1.

Diseases measures at baseline (Table 1A), stratified according to ASAS HI states at week 16 and 52 (Table 1B), changes from week 0 to 16 and 52 (Table 1C) and responsiveness (Table 1D).

Table 1ATable 1BTable 1CTable 1DBaselineASAS HI at week 16ASAS HI at week 52Absolute change in ASAS HI week 0 to 16Percentage change in ASAS HI week 0 to 16Responsiveness week 0-160-56-170-56-17<3≥3<30%≥30%SRMESn=45n=22n=22n=26n=16n=18n=26n=16n=28n=45n=45ASAS HI10.0 (8;11)1.5*** (1;4)8.0 (7;10)2.0*** (0.8;3.3)9.5 (7;10.8)-1.5*** (-2;2)-6.0 (-12;-3)-1*** (-2;2)-5.5 (-12;-2)1.61.3ASDAS3.7 (3.1;4.2)1*** (0.9;1.5)2.1 (1.1;3.1)1.2*** (0.8;1.5)2.2 (1.8;3.3)-1.3*** (-2.5;1)-2.2 (-4.6;-1.3)-1.2*** (-2.5;1)-2.2 (-4.6;-1.3)2.51.7BASDAI6.1 (5;7.20.9*** (0.5;2.3)3.2 (1.8;5.1)1.3*** (0.3;2.3)3.8 (2.9;5.7)-1.7*** (-5.3;0.9)-4.9 (-6.7;-1.9)-1.6*** (-5.3;0.9)-4.8 (-6.7;-1.9)2.71.8BASFI4.4 (3;5.90.6*** (0.3;1.4)2.3 (1.4;4)0.3*** (0.1;1.4)2.5 (1.5;3.3)-1.2*** (-4.4;1.2)-3.5 (-6.7;-0.2)-1.1*** (-3.9;1.2)-3.5 (-6.7;-0.15)1.41.4BASMI2;0 (1;3)1.0 (0;2)1.0 (0;2)1.0 (0;2)1.0 (0;3)0 (-3;2)-1.0 (-4;2)0 (-3;2)-1.0 (-4;2)0.40.6Pain7.0 (5.6;8.1)0.8*** (0.3;1.2)2.9 (1.3;5.5)0.7** (0.3;2.6)3.3 (1.1;6.3)-2.6** (-8.8;1.9)-5.6 (-8.6;-1.1)-1.8*** (-6.8;1.9)-5.6 (-8.8;-1.1)2.71.8Pt. global7.5 (6.4;8.4)1.0*** (0.4;1.9)3.0 (1.3;6.7)0.6*** (0.2;2.1)4.4 (2.3;6.9)-3.4*** (-6.5;0.8)-6.7 (-8.8;-1.1)-2.8*** (-6.3;0.8)-6.5 (-8.8;-1.1)3.31.8CRP (mg/l)7.7 (0.9;22)0.3* (0.3;2.2)1.3 (0.3;8.5)0.3** (0.3;2.5)1.0 (0.3;5)-1.7 (-39.6;6.9)-5.2 (-79.7;19)-1.7 (-39.6;6.9)-5.2 (-79.7;19)0.50.6SPARCC MRI SIJ inflammation14 (4;24.5)4.0 (0;6.5)2.0 (0;7.8)2.0 (0;4.3)2.0 (1;6)-5.5 (-30;2)-12.5 (-36;0)-5.5 (-30;2)-12.5 (-36;0)0.91.1SPARCC MRI spine infl.8 (4;15)0 (0;3.5)1.0 (0;4.3)0(0;2)1.0 (0;3)-2.5** (-98;2)-8 (-55;0)-2.5* (-98;2)-8 (-55;0)0.50.7

Median (IQR). Mann-Whitney test. * p<0.05. ** p<0.01. *** p<0.001. Standardized response mean (SRM) and effect size (ES) ≥0.50 to <0.80 and ≥0.80 represents moderate and high responsiveness.

Conclusion

ASAS HI showed good construct validity and responsiveness.

References

[1]Kiltz U. ARD 2015;74:830

[2]Kiltz U. ARD 2018;77:1311

[3]Krabbe. Rheumatology 2020;59:3358

[4]Walsh. ACR 2020 doi: 10.1002/acr.24482

[5]Molto. ARD 2021;80(11):1436

Disclosure of Interests

Susanne Juhl Pedersen Speakers bureau: MSD, Pfizer, AbbVie, Novartis and UCB.

Grant/research support from: AbbVie, MSD, and Novartis., Inge Juul Sørensen: None declared, Bente Jensen: None declared, Ole Madsen: None declared, Mette Klarlund: None declared, Jakob Møllenbach Møller: None declared, Mats Peter Johansson: None declared, Kasper K Gosvig: None declared, Mikkel Østergaard Speakers bureau: Abbvie, BMS, Celgene, Eli-Lilly, Galapagos, Gilead, Janssen, Merck, Novartis, Orion, Pfizer, Roche and UCB., Consultant of: Abbvie, BMS, Boehringer-Ingelheim, Celgene, Eli-Lilly, Hospira, Janssen, Merck, Novartis, Novo, Orion, Pfizer, Regeneron, Roche, Sandoz, Sanofi and UCB., Grant/research support from: Abbvie, Amgen, BMS, Merck, Celgene and Novartis.

AB1350 CAN DIFFUSION-WEIGHTED MRI REPLACE INTRAVENOUS GADOLINIUM CONTRAST-ENHANCED MRI FOR ASSESSMENT OF SYNOVITIS?

Background

In clinical trials of rheumatoid arthritis (RA) patients, intravenous gadolinium contrast injection is the gold standard method for MRI assessment of synovitis, e.g. by the OMERACT RA MRI Scoring method (RAMRIS). It has been shown that diffusion-weighted MRI (DW-MRI) allows visualization of synovitis1.

Objectives

To establish a method for measuring MRI-derived apparent diffusion coefficient (ADC) from DW-MRI and to test its correlation with RAMRIS synovitis scoring.

Methods

MRI including diffusion-weighting of the dominant hand was performed in a cohort of RA patients in clinical remission (disease activity score in 28 joints-C-reactive protein [DAS28-CRP] <3.2 and no swollen joints). ADC measurements of the synovium were assessed in 7 areas (3 wrist joint areas and 4 metacarpophalangeal (MCP) joints), similar to the RAMRIS. Intra-observer agreement for the ADC reading was determined using the intraclass correlation coefficient (ICC). Spearman’s rho (ρ) was calculated for the correlation of ADC with RAMRIS Synovitis. Differences in mean ADC between the individual RAMRIS synovitis grades were examined using ANOVA with Bonferroni correction for multiple tests.

Results

In 63 patients (67% females, age mean 61.0 years (range 36-78 years), disease duration 11.9 years, 0-59 years), DAS28-CRP 2.1 (1.6-3.0) the total RAMRIS synovitis was mean 5.8 (range 0-18). The mean ADC was 0.98x10-3 mm2/s (0.11-2.80). Correlations between RAMRIS synovitis and ADC in the 7 joint areas and mean differences in ADC between RAMRIS synovitis grades are presented in the Table 1. When all 7 joints were pooled the mean ADC and RAMRIS synovitis were moderately positively correlated, ρ=0.49; p<0.01. Statistically significant differences (p<0.01) in mean ADC were observed between all RAMRIS synovitis grades (0 vs 1, 0 vs 2, etc) except for the difference between grade 2 and 3. Good intra-observer (ICC = 0.62 (95%CI 0.49-0.72)) was found.

Table 1.All jointsRUJRCJCMCJMCP2MCP3MCP4MCP5RAMRIS synovitis vs ADC correlation, (Spearman’s rho)0.49; p<0.010.39; p<0.010.34; p=0.010.37; p<0.010.59; p<0.010.46; p<0.010.69; p<0.010.42; p<0.01Mean differences in ADC [x10-3 mm2/s]between RAMRIS synovitis grades(ANOVA with Bonferroni correction)0-1-0.20, p<0.01-0.29, p=0.310.09, p=1.00-0.14, p=1.00-0.04, p=1.000.02, p=1.00-0.42, p<0.01n/a0-2-0.55, p<0.01-0.28, p=0.91-0.15, p=1.00-0.27, p=0.43-0.38, p=0.03-0.47, p<0.01-0.62, p<0.01n/a0-3-0.79, p<0.01-0.87, p<0.01-0.20, p=1.00-0.01, p=1.00-0.72, p<0.01-0.57, p<0,01-0.93, p<0.01n/a1-2-0.34, p<0.010.14, p=1.00-0.25, p=0.70-0.13, p=1.00-0.34, p=0.1-0.49, p<0,01-0.19, p=1.00n/a1-3-0.59, p<0.01-0.58, p=0.26-0.29, p=1.000.13, p=1.00-0.68, p<0.01-0.59, p<0.01-0.51, p=0.02n/a2-3-0.24, p=0.09-0.60, p=0.24-0.05, p=1.000.26, p=1.00-0.34, p=0.120.10, p=1.00-0.31, p=0.63n/aIntra-observer ICC (95%CI)0,62 (0,49:0,72)0.70 (0.34:0.89)0.57 (0.14:0.82)0.39 (0.14:0.74)0.81 (0.53:0.93)0.70 (0.34:0.89)(0.81 (0.51:0.93)0.40 (0.18:0.74)

ADC: Apparent diffusion coefficient, CI: confidence interval, CMCJ: carpo-metacarpal joint, ICC: intraclass correlation coefficient, MCP: metacarpo-phalangeal joint, RCJ: radio-carpal joint, RUJ: radio-ulnar joint

Conclusion

ADC, determined from DWI-MRI, may be used to grade synovitis without the use of gadolinium contrast injection.

References

[1]Li et al Magn Reson Imaging. 2014 May;32:350-3.

Disclosure of Interests

Jakob Møllenbach Møller: None declared, Karen Lind Gandrup: None declared, Mikkel Østergaard Speakers bureau: Abbvie, BMS, Celgene, Eli-Lilly, Galapagos, Gilead, Janssen, Merck, Novartis, Orion, Pfizer, Roche and UCB, Consultant of: Abbvie, BMS, Boehringer-Ingelheim, Celgene, Eli-Lilly, Hospira, Janssen, Merck, Novartis, Novo, Orion, Pfizer, Regeneron, Roche, Sandoz, Sanofi and UCB, Grant/research support from: Abbvie, Amgen, BMS, Merck, Celgene and Novartis, Daniel Glinatsi Speakers bureau: Eli Lilly, Consultant of: AbbVie, Ole Madsen: None declared, Kim Hørslev-Petersen: None declared, Signe Møller-Bisgaard: None declared

POS0550 LONG TERM EFFICACY OF A 2-YEAR MRI TREAT-TO-TARGET STRATEGY ON DISEASE ACTIVITY, MRI INFLAMMATION AND PHYSICAL FUNCTION IN RHEUMATOID ARTHRITIS PATIENTS IN CLINICAL REMISSION: FIVE YEAR FOLLOW-UP OF THE IMAGINE RA-COHORT

Background

Targeting MRI remission in rheumatoid arthritis (RA) patients in clinical remission may improve long term clinical, functional and MRI outcomes.

Objectives

To investigate whether a 2-year treat-to-target (T2T) strategy, based on structured MRI assessments targeting absence of osteitis combined with clinical remission, compared with a conventional clinical T2T strategy targeting clinical remission only, improves disease activity, physical function and suppresses MRI-inflammation over 5 years in RA patients.

Methods

The IMAGINE-more trial was designed as an extension protocol to the 2-year IMAGINE-RA randomised controlled trial (RCT). IMAGINE-RA included 200 RA patients, in clinical remission (DAS28-CRP<3.2 and no swollen joints), who received conventional synthetic disease-modifying antirheumatic drugs (csDMARD) and investigated whether an MRI T2T strategy targeting absence of osteitis in combination with clinical remission (DAS28-CRP≤3.2 and no swollen joints) could increase remission rates and prevent erosive progression compared with a conventional T2T strategy targeting clinical remission only. If target was not met, treatment was escalated according to a predefined treatment algorithm starting with increment in csDMARDs and then adding biologics. At the end of the study, participants were invited to participate in the IMAGINE-more follow-up study. Patients were managed in routine outpatient clinic and had three IMAGINE-more visits including clinical examination (year 3, 4 and 5) and contrast-enhanced MRI of the dominant wrist and 2nd-5th metacarpophalangeal joints (year 3 and 5). The primary clinical endpoint was the proportion of patients achieving DAS28-CRP remission (DAS28-CRP<2.6) at year 5. Predefined key secondary outcomes were disease activity (DAS28-CRP), and changes in MRI osteitis (OMERACT RA MRI scoring system (RAMRIS)) and functional level (Health Assessment Questionnaire (HAQ)) from baseline to 5-years follow up. Endpoints were analysed by logistic regression models and repeated measures mixed effects models adjusted for propensity scores corresponding to (remaining in) group allocation.

Results

Fifty-nine patients in the MRI T2T arm and 72 patients in conventional T2T arm consented to participate. Of these, 47 patients (80%) in the MRI T2T group and 54 patients (75%) in the conventional T2T group reached the primary clinical endpoint (p=0.161) (Table 1 and Figure 1). No statistically significant differences between treatment strategies in key secondary outcomes were seen.

Table 1.

Primary and key secondary outcomes at 5 years

MRI T2TConventional T2TDifference between groupsP valueN=59N=72Primary endpointDAS28-CRP remission (DAS28-CRP<2.6), No. (%)47 (80%)54 (75%)2.00 (0.76 to 5.28)0.161Key secondary endpointsDAS28-CRP1.79 (0.08)1.94 (0.08)-0.15 (-0.38 to 0.07)0.176Change from baseline in MRI osteitis (RAMRIS)-0.17 (0.58)0.18 (0.54)-0.35 (-1.96 to 1.25)0.663Change from baseline in HAQ-0.02 (0.03)0.05 (0.03)-0.07 (-0.15 to 0.01)0.080

Group estimates are presented as No. (%) for dichotomous data and least squares means (SE) for continuous data. For the primary endpoint, adjusted odds ratio and 95%CI between groups were calculated from a logistic regression model including a fixed factor for treatment arm, and an adjustment for propensity score as a covariate. For endpoints with continuous data, least squares mean differences between groups were calculated based on repeated-measures mixed linear models adjusted for baseline values and propensity scores.

Conclusion

A 2-year MRI T2T strategy targeting absence of MRI osteitis combined with clinical remission as compared to a conventional clinical T2T strategy in RA patients had no effect on the long-term probability of achieving DAS28-CRP remission. These findnings do not support the use of an MRI-guided strategy for treating patients with RA.

References

[1]Møller-Bisgaard S et al: JAMA 2019, 321(5):461-472.

Disclosure of Interests

Signe Møller-Bisgaard Grant/research support from: AbbVie, Kim Hørslev-Petersen: None declared, Daniel Glinatsi: None declared, Bo Ejbjerg: None declared, Merete L. Hetland: None declared, Jakob Møllenbach Møller: None declared, Robin Christensen: None declared, Sabrina Mai Nielsen: None declared, Mikael Boesen: None declared, Kristian Stengaard-Pedersen: None declared, Ole Madsen: None declared, Bente Jensen: None declared, Jan Alexander Villadsen: None declared, Ellen Margrethe Hauge: None declared, Oliver Hendricks: None declared, Hanne Merete Lindegaard: None declared, Niels Steen Krogh: None declared, Anne Grethe Jurik: None declared, Henrik Thomsen: None declared, Mikkel Østergaard Speakers bureau: Abbvie, BMS, Celgene, Eli-Lilly, Galapagos, Gilead, Janssen, Merck, Novartis, Orion, Pfizer, Roche and UCB, Consultant of: Abbvie, BMS, Boehringer-Ingelheim, Celgene, Eli-Lilly, Hospira, Janssen, Merck, Novartis, Novo, Orion, Pfizer, Regeneron, Roche, Sandoz, Sanofi and UCB, Grant/research support from: Abbvie, Amgen, BMS, Merck, Celgene and Novartis.

Fine Mapping of a Major Backfat QTL Reveals a Causal Regulatory Variant Affecting the CCND2 Gene

Backfat is an important trait in pork production, and it has been included in the breeding objectives of genetic companies for decades. Although adipose tissue is a good energy storage, excessive fat results in reduced efficiency and economical losses. A large QTL for backfat thickness on chromosome 5 is still segregating in different commercial pig breeds. We fine mapped this QTL region using a genome-wide association analysis (GWAS) with 133,358 genotyped animals from five commercial populations (Landrace, Pietrain, Large White, Synthetic, and Duroc) imputed to the porcine 660K SNP chip. The lead SNP was located at 5:66103958 (G/A) within the third intron of the CCND2 gene, with the G allele associated with more backfat, while the A allele is associated with less backfat. We further phased the QTL region to discover a core haplotype of five SNPs associated with low backfat across three breeds. Linkage disequilibrium analysis using whole-genome sequence data revealed three candidate causal variants within intronic regions and downstream of the CCND2 gene, including the lead SNP. We evaluated the association of the lead SNP with the expression of the genes in the QTL region (including CCND2) in a large cohort of 100 crossbred samples, sequenced in four different tissues (lung, spleen, liver, muscle). Results show that the A allele increases the expression of CCND2 in an additive way in three out of four tissues. Our findings indicate that the causal variant for this QTL region is a regulatory variant within the third intron of the CCND2 gene affecting the expression of CCND2.

Evaluation and Comparison of Ultrasonic and UWB Technology for Indoor Localization in an Industrial Environment

Evaluations of different technologies and solutions for indoor localization exist but only a few are aimed at the industrial context. In this paper, we compare and analyze two prominent solutions based on Ultra Wide Band Radio (Pozyx) and Ultrasound (GoT), both installed in an industrial manufacturing laboratory. The comparison comprises a static and a dynamic case. The static case evaluates average localization errors over 90 s intervals for 100 ground-truth points at three different heights, corresponding to different relevant objects in an industrial environment: mobile robots, pallets, forklifts and worker helmets. The average error obtained across the laboratory is similar for both systems and is between 0.3 m and 0.6 m, with higher errors for low altitudes. The dynamic case is performed with a mobile robot travelling with an average speed of 0.5 m/s at a height of 0.3 m. In this case, low frequency error components are filtered out to focus the comparison on dynamic errors. Average dynamic errors are within 0.3–0.4 m for Pozyx and within 0.1–0.2 m for GoT. Results show an acceptable accuracy required for tracking people or objects and could serve as a guideline for the least achievable accuracy when applied for mobile robotics in conjunction with other elements of a robotic navigation stack.

The Role of Feed Restriction on DNA Methylation, Feed Efficiency, Metabolome, Biochemical Profile, and Progesterone Patterns in the Female Filial Generation (F1) Obtained From Early Feed Restricted Ewes (F0)

Deficient management of replacement animals in the farm during early developmental windows may promote adverse programming effects on reproductive traits and subsequent transmission to the next generation. In this sense, DNA methylation profiles allow researchers to decode epigenetic regulation mechanisms in mammals and identify novel candidate genes correlated with phenotype differences in both dams and offspring. Therefore, improving knowledge in the field of epigenetics and intergenerational effects caused by prenatal and postnatal early nutritional events (e.g., feed restriction) is crucial for refining strategies dedicated to animal breeding. In this study, we determined differences in the global blood methylation patterns, biochemical profile, and metabolome of ewe lambs (F1) born from either early feed restricted dams (F0-RES) or fed ad libitum (F0-ADL). Our data show that functional categories such as those related to cellular processes, phosphorylation, nervous system, immunity response, or reproductive function were enriched significantly in the F1-RES lambs due to differences in the methylation of genes in these categories. These F1-RES lambs did not show differences in feed efficiency during the replacement period but presented higher levels of insulin and triglycerides and reduced concentration of progesterone, whereas the metabolome profile demonstrated variations in the bile acid composition when compared with the F1-ADL lambs. Taken together, all these results suggest that intergenerational effects caused by early feed restriction of dams (F0) may persist in the F1 female lambs with negative consequences on genes involved in cellular processes and reproductive traits.

Time Course Transcriptomic Study Reveals the Gene Regulation During Liver Development and the Correlation With Abdominal Fat Weight in Chicken

Background: The liver is the central metabolic organ of animals. In chicken, knowledge on the relationship between gene expression in the liver and fat deposition during development is still limited. A time-course transcriptomic study from the embryonic (day 12) to the egg-producing period (day 180 after hatch) was performed to profile slow-growing meat type chicken liver gene expression and to investigate its correlation with abdominal fat deposition. Results: The transcriptome profiles showed a separation of the different developmental stages. In total, 13,096 genes were ubiquitously expressed at all the tested developmental stages. The analysis of differentially expressed genes between adjacent developmental stages showed that biosynthesis of unsaturated fatty acids pathway was enriched from day 21 to day 140 after hatch. The correlation between liver gene expression and the trait abdominal fat weight (AFW) was analyzed by weighted gene co-expression network analysis. The genes MFGE8, HHLA1, CKAP2, and ACSBG2 were identified as hub genes in AFW positively correlated modules, which suggested important roles of these genes in the lipid metabolism in chicken liver. Conclusion: Our results provided a resource of developmental transcriptome profiles in chicken liver and suggested that the gene ACSBG2 among other detected genes can be used as a candidate gene for selecting low AFW chickens.

Organoids: a promising new in vitro platform in livestock and veterinary research

Organoids are self-organizing, self-renewing three-dimensional cellular structures that resemble organs in structure and function. They can be derived from adult stem cells, embryonic stem cells, or induced pluripotent stem cells. They contain most of the relevant cell types with a topology and cell-to-cell interactions resembling that of the in vivo tissue. The widespread and increasing adoption of organoid-based technologies in human biomedical research is testament to their enormous potential in basic, translational- and applied-research. In a similar fashion there appear to be ample possibilities for research applications of organoids from livestock and companion animals. Furthermore, organoids as in vitro models offer a great possibility to reduce the use of experimental animals. Here, we provide an overview of studies on organoids in livestock and companion animal species, with focus on the methods developed for organoids from a variety of tissues/organs from various animal species and on the applications in veterinary research. Current limitations, and ongoing research to address these limitations, are discussed. Further, we elaborate on a number of fields of research in animal nutrition, host-microbe interactions, animal breeding and genomics, and animal biotechnology, in which organoids may have great potential as an in vitro research tool.

Genetic consequences of long-term small effective population size in the critically endangered pygmy hog

Increasing human disturbance and climate change have a major impact on habitat integrity and size, with far-reaching consequences for wild fauna and flora. Specifically, population decline and habitat fragmentation result in small, isolated populations. To what extend different endangered species can cope with small population size is still largely unknown. Studies on the genomic landscape of these species can shed light on past demographic dynamics and current genetic load, thereby also providing guidance for conservation programs. The pygmy hog (Porcula salvania) is the smallest and rarest wild pig in the world, with current estimation of only a few hundred living in the wild. Here, we analyzed whole-genome sequencing data of six pygmy hogs, three from the wild and three from a captive population, along with 30 pigs representing six other Suidae. First, we show that the pygmy hog had a very small population size with low genetic diversity over the course of the past ~1 million years. One indication of historical small effective population size is the absence of mitochondrial variation in the six sequenced individuals. Second, we evaluated the impact of historical demography. Runs of homozygosity (ROH) analysis suggests that the pygmy hog population has gone through past but not recent inbreeding. Also, the long-term, extremely small population size may have led to the accumulation of harmful mutations suggesting that the accumulation of deleterious mutations is exceeding purifying selection in this species. Thus, care has to be taken in the conservation program to avoid or minimize the potential for further inbreeding depression, and guard against environmental changes in the future.

Determining manufacturing system changes based on new product specifications

Purpose

The purpose of this paper is to investigate how necessary changes in a manufacturing system can be determined based on a new product specification. It proposes a formal modelling approach, enhancing the utilization of changeability of a manufacturing system given a set of changes in a product.

Design/methodology/approach

To develop the proposed modelling approach, a design science research method is used to iteratively frame an issue, develop a solution and evaluate it in a relevant environment. Evaluation is carried out through a case study.

Findings

A stepwise method is introduced, facilitating the creation of a model describing the relations between product characteristics within a product family and the changeability of a manufacturing system. Limitations of each manufacturing system module are evaluated to determine permittable changes in the product domain. This establishes clear relations between product attributes and manufacturing capabilities. Through this, users receive feedback on which parts of the manufacturing system must change, depending on changes in product attributes.

Research limitations/implications

Testing has been carried out in an academic learning factory setting. Products and processes are thus less complicated than an industrial setting. The system used for validation is highly modular by design.

Practical implications

The proposed approach could be used during product development, when determining characteristics and variety of new products, evaluating the consequences of changing the solution space. This implies a shorter time-to-market and lower product costs.

Social implications

Faster product development and shorter time-to-market would give manufacturers increased agility to track market needs, and ultimately lead to greater fulfilment of customer requirements.

Originality/value

The current body of literature focus on modelling either products or manufacturing systems. Little literature addresses both, but does not touch on identifying changes within parts of the manufacturing system, nor supports the high changeability proposed in this research.

Genome-Wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO2 Levels

Temperature and CO₂ concentration during incubation have profound effects on broiler chick development, and numerous studies have identified significant effects on hatch heart weight (HW) as a result of differences in these parameters. Early life environment has also been shown to affect broiler performance later in life; it has thus been suggested that epigenetic mechanisms may mediate long-term physiological changes induced by environmental stimuli. DNA methylation is an epigenetic modification that can confer heritable changes in gene expression. Using reduced-representation bisulfite sequencing (RRBS), we assessed DNA methylation patterns in cardiac tissue of 84 broiler hatchlings incubated at two egg shell temperatures (EST; 37.8°C and 38.9°C) and three CO₂ concentrations (0.1%, 0.4%, and 0.8%) from day 8 of incubation onward. We assessed differential methylation between EST treatments and identified 2,175 differentially methylated (DM) CpGs (1,121 hypermethylated, 1,054 hypomethylated at 38.9° vs. 37.8°) in 269 gene promoters and 949 intragenic regions. DM genes (DMGs) were associated with heart developmental processes, including cardiomyocyte proliferation and differentiation. We identified enriched binding motifs among DM loci, including those for transcription factors associated with cell proliferation and heart development among hypomethylated CpGs that suggest increased binding ability at higher EST. We identified 9,823 DM CpGs between at least two CO₂ treatments, with the greatest difference observed between 0.8 and 0.1% CO₂ that disproportionately impacted genes involved in cardiac muscle development and response to low oxygen levels. Using HW measurements from the same chicks, we performed an epigenome-wide association study (EWAS) for HW, and identified 23 significantly associated CpGs, nine of which were also DM between ESTs. We found corresponding differences in transcript abundance between ESTs in three DMGs (ABLIM2, PITX2, and THRSP). Hypomethylation of an exonic CpG in PITX2 at 38.9°C was associated with increased expression, and suggests increased cell proliferation in broiler hatchlings incubated at higher temperatures. Overall, these results identified numerous epigenetic associations between chick incubation factors and heart development that may manifest in long-term differences in animal performance.

RNA-Seq Analysis Reveals Hub Genes Involved in Chicken Intramuscular Fat and Abdominal Fat Deposition During Development

Fat traits are important in the chicken industry where there is a desire for high intramuscular fat (IMF) and low abdominal fat. However, there is limited knowledge on the relationship between the dynamic status of gene expression and the body fat deposition in chicken. Transcriptome data were obtained from breast muscle and abdominal fat of female chickens from nine developmental stages (from embryonic day 12 to hatched day 180). In total, 8,545 genes in breast muscle and 6,824 genes in abdominal fat were identified as developmentally dynamic genes. Weighted correlation network analysis was used to identify gene modules and the hub genes. Twenty-one hub genes were identified, e.g., ENSGALG00000041996, which represents a candidate for high IMF, and CREB3L1, which relates to low abdominal fat weight. The transcript factor L3MBTL1 and the transcript factor cofactors TNIP1, HAT1, and BEND6 related to both high breast muscle IMF and low abdominal fat weight. Our results provide a resource of developmental transcriptome profiles in chicken breast muscle and abdominal fat. The candidate genes can be used in the selection for increased IMF content and/or a decrease in abdominal fat weight which would contribute to the improvement of these traits.

Congruence of Transcription Programs in Adult Stem Cell-Derived Jejunum Organoids and Original Tissue During Long-Term Culture

The emergence of intestinal organoids, as a stem cell-based self-renewable model system, has led to many studies on intestinal development and cell-cell signaling. However, potential issues regarding the phenotypic stability and reproducibility of the methodology during culture still needs to be addressed for different organoids. Here we investigated the transcriptomes of jejunum organoids derived from the same pig as well as batch-to-batch variation of organoids derived from different pigs over long-term passage. The set of genes expressed in organoids closely resembled that of the tissue of origin, including small intestine specific genes, for at least 17 passages. Minor differences in gene expression were observed between individual organoid cultures. In contrast, most small intestine-specific genes were not expressed in the jejunum cell line IPEC-J2, which also showed gene expression consistent with cancer phenotypes. We conclude that intestinal organoids provide a robust and stable model for translational research with clear advantages over transformed cells.

SAT0548 DEVELOPMENT AND VALIDATION OF THREE PRELIMINARY MRI SACROILIAC JOINT COMPOSITE STRUCTURAL DAMAGE SCORES IN A 5-YEAR LONGITUDINAL STUDY OF PATIENTS WITH AXIAL SPONDYLOARTHRITIS

Background:

In axial spondyloarthritis (axSpA), MRI reliably detects structural lesions in the sacroiliac joints (SIJs). The SPARCC SIJ Structural Score (SSS)(1) is a reliable and validated method to assess the individual structural lesions of the SIJs, i.e. fat lesion, erosion, backfill (fat metaplasia in an erosion cavity) and ankylosis. Several MRI studies have indicated that bone destruction, i.e. erosion, is often followed by formation of new bone in the erosion cavity (backfill), ultimately leading to ankylosis(2).

Objectives:

The aim was to combine SPARCC SSS for erosion, backfill and ankylosis into a composite score for SIJ structural damage and to test this score in a 5-year follow up study.

Methods:

Thirty-three patients fulfilling ASAS criteria for axSpA were followed for 5 years after initiation of TNF inhibitor in the BIOSPA study(3). T1-weighted and STIR MRI sequences of the SIJs acquired at week 0, 46 and year 2, 3, 4, 5 were evaluated with SPARCC SSS. In each of 5 slices of each SIJ, erosion is scored 0-1 per joint quadrant (score range 0-40), backfill 0-1 per joint half (score range 0-20) and ankylosis 0-1 per joint half (score range 0-20). Based on the scores for erosion, backfill and ankylosis 3 versions of a preliminary Composite axSpA MRI SIJ Structural Damage Score (CSDS) were calculated:

CSDS–A: (erosion score x0.5) + backfill score + ankylosis score

CSDS–B: (erosion score x1) + (backfill score x4) + (ankylosis score x6)

CSDS–C: (erosion score x1) < (backfill score x4) < (ankylosis score x6)

The “<” indicates a hierarchical order, meaning that erosion was not scored if backfill was present in the same joint half and erosion and backfill were not scored if ankylosis was present in the joint half.

Results:

Patients were divided into two groups: patients with almost complete bilateral ankylosis (baseline SPARCC SSS Ankylosis ≥18, n=10) and patients with no/minor ankylosis (baseline SPARCC SSS Ankylosis ≤7, n=23). At baseline patients with no/minor ankylosis were younger, had shorter symptom duration, lower BASMI, higher SPARCC SIJ Inflammation, lower SSS Fat, Erosion, Backfill and Ankylosis, as compared with patients with almost complete ankylosis.

At baseline, CSDS-A, -B and -C correlated positively with SPARCC SSS Fat and Ankylosis and modified New York criteria grading, and negatively with BASDAI and SPARCC inflammation. Change in CSDS-B and -C over 5 years correlated positively with change in SSS Fat and Ankylosis and negatively with change in SPARCC Inflammation. There was no change in the group with almost complete ankylosis.

The annual progression for CSDS-B and -C was statistically significantly larger in year 1 compared with year 4 (p=0.01) and numerically larger compared with year 2 (p=0.075), 3 (p=0.382) and 5 (p=0.073). Figure 1 shows the annual change in patients with no/minor ankylosis.

Conclusion:

Three preliminary Composite Structural Damage Scores for MRI assessment of the SIJs in patients with axSpA, which allows scoring of MRI progression of erosion through backfill to ankylosis, were introduced. Progression was most pronounced the first year after TNF inhibitor initiation. This novel approach may be useful for monitoring structural progression in axSpA. We suggest that these methods are further tested for responsiveness and ability to differentiate between different therapies in randomized controlled trials.

References:

[1]Maksymowych WP et al. J Rheum 2015;42:79-86.

[2]Maksymowych WP et al. Art Rheum 2014;66:2958-67.

[3]Pedersen SJ et al. Scand J Rheum 2019;48:185-197.

Disclosure of Interests:

Marie Wetterslev: None declared, Mikkel Ǿstergaard Grant/research support from: AbbVie, Bristol-Myers Squibb, Celgene, Merck, and Novartis, Consultant of: AbbVie, Bristol-Myers Squibb, Boehringer Ingelheim, Celgene, Eli Lilly, Hospira, Janssen, Merck, Novartis, Novo Nordisk, Orion, Pfizer, Regeneron, Roche, Sandoz, Sanofi, and UCB, Speakers bureau: AbbVie, Bristol-Myers Squibb, Boehringer Ingelheim, Celgene, Eli Lilly, Hospira, Janssen, Merck, Novartis, Novo Nordisk, Orion, Pfizer, Regeneron, Roche, Sandoz, Sanofi, and UCB, Inge Juul Sørensen: None declared, Ulrich Weber: None declared, Anne Gitte Loft Grant/research support from: Novartis, Consultant of: AbbVie, MSD, Novartis, Pfizer and UCB, Speakers bureau: AbbVie, MSD, Novartis, Pfizer and UCB, Gina Kollerup Speakers bureau: Eli Lilly, Lars Juul: None declared, Gorm Thamsborg: None declared, Ole Madsen: None declared, Jakob Møllenbach Møller: None declared, Susanne Juhl Pedersen Grant/research support from: Novartis

Altered Hippocampal Epigenetic Regulation Underlying Reduced Cognitive Development in Response to Early Life Environmental Insults

The hippocampus is involved in learning and memory and undergoes significant growth and maturation during the neonatal period. Environmental insults during this developmental timeframe can have lasting effects on brain structure and function. This study assessed hippocampal DNA methylation and gene transcription from two independent studies reporting reduced cognitive development stemming from early life environmental insults (iron deficiency and porcine reproductive and respiratory syndrome virus (PRRSv) infection) using porcine biomedical models. In total, 420 differentially expressed genes (DEGs) were identified between the reduced cognition and control groups, including genes involved in neurodevelopment and function. Gene ontology (GO) terms enriched for DEGs were associated with immune responses, angiogenesis, and cellular development. In addition, 116 differentially methylated regions (DMRs) were identified, which overlapped 125 genes. While no GO terms were enriched for genes overlapping DMRs, many of these genes are known to be involved in neurodevelopment and function, angiogenesis, and immunity. The observed altered methylation and expression of genes involved in neurological function suggest reduced cognition in response to early life environmental insults is due to altered cholinergic signaling and calcium regulation. Finally, two DMRs overlapped with two DEGs, VWF and LRRC32, which are associated with blood brain barrier permeability and regulatory T-cell activation, respectively. These results support the role of altered hippocampal DNA methylation and gene expression in early life environmentally-induced reductions in cognitive development across independent studies.

Cut & recombine: reuse of robot action components based on simple language instructions

Human beings can generalize from one action to similar ones. Robots cannot do this and progress concerning information transfer between robotic actions is slow. We have designed a system that performs action generalization for manipulation actions in different scenarios. It relies on an action representation for which we perform code-snippet replacement, combining information from different actions to form new ones. The system interprets human instructions via a parser using simplified language. It uses action and object names to index action data tables (ADTs), where execution-relevant information is stored. We have created an ADT database from three different sources (KUKA LWR, UR5, and simulation) and show how a new ADT is generated by cutting and recombining data from existing ADTs. To achieve this, a small set of action templates is used. After parsing a new instruction, index-based searching finds similar ADTs in the database. Then the action template of the new action is matched against the information in the similar ADTs. Code snippets are extracted and ranked according to matching quality. The new ADT is created by concatenating code snippets from best matches. For execution, only coordinate transforms are needed to account for the poses of the objects in the new scene. The system was evaluated, without additional error correction, using 45 unknown objects in 81 new action executions, with 80% success. We then extended the method including more detailed shape information, which further reduced errors. This demonstrates that cut & recombine is a viable approach for action generalization in service robotic applications.

Genomic analysis on pygmy hog reveals extensive interbreeding during wild boar expansion

Wild boar (Sus scrofa) drastically colonized mainland Eurasia and North Africa, most likely from East Asia during the Plio-Pleistocene (2–1Mya). In recent studies, based on genome-wide information, it was hypothesized that wild boar did not replace the species it encountered, but instead exchanged genetic materials with them through admixture. The highly endangered pygmy hog (Porcula salvania) is the only suid species in mainland Eurasia known to have outlived this expansion, and therefore provides a unique opportunity to test this hybridization hypothesis. Analyses of pygmy hog genomes indicate that despite large phylogenetic divergence (~2 My), wild boar and pygmy hog did indeed interbreed as the former expanded across Eurasia. In addition, we also assess the taxonomic placement of the donor of another introgression, pertaining to a now-extinct species with a deep phylogenetic placement in the Suidae tree. Altogether, our analyses indicate that the rapid spread of wild boar was facilitated by inter-specific/inter-generic admixtures.

The pygmy hog (Porcula salvania), now highly endangered and restricted in a small region at the southern foothills of the Himalaya, is the only suid species in mainland Eurasia that outlived the expansion of wild boar (Sus scrofa). Here, the authors analyze genomes of pygmy hog and related suid species, and identify signals of introgression among these species.

Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome

Livestock populations can be used to study recessive defects caused by deleterious alleles. The frequency of deleterious alleles including recessive lethal alleles can stay at high or moderate frequency within a population, especially if recessive lethal alleles exhibit an advantage for favourable traits in heterozygotes. In this study, we report such a recessive lethal deletion of 212kb (del) within the BBS9 gene in a breeding population of pigs. The deletion produces a truncated BBS9 protein expected to cause a complete loss-of-function, and we find a reduction of approximately 20% on the total number of piglets born from carrier by carrier matings. Homozygous del/del animals die mid- to late-gestation, as observed from high increase in numbers of mummified piglets resulting from carrier-by-carrier crosses. The moderate 10.8% carrier frequency (5.4% allele frequency) in this pig population suggests an advantage on a favourable trait in heterozygotes. Indeed, heterozygous carriers exhibit increased growth rate, an important selection trait in pig breeding. Increased growth and appetite together with a lower birth weight for carriers of the BBS9 null allele in pigs is analogous to the phenotype described in human and mouse for (naturally occurring) BBS9 null-mutants. We show that fetal death, however, is induced by reduced expression of the downstream BMPER gene, an essential gene for normal foetal development. In conclusion, this study describes a lethal 212kb deletion with pleiotropic effects on two different genes, one resulting in fetal death in homozygous state (BMPER), and the other increasing growth (BBS9) in heterozygous state. We provide strong evidence for balancing selection resulting in an unexpected high frequency of a lethal allele in the population. This study shows that the large amounts of genomic and phenotypic data routinely generated in modern commercial breeding programs deliver a powerful tool to monitor and control lethal alleles much more efficiently.

We report a large deletion within the BBS9 gene that induces late fetal mortality in homozygous affected animals in a commercial pig population. This late fetal mortality causes the fetus to become encapsulated and desiccated during the remaining time of the pregnancy, a process called mummification. The unusually high carrier frequency for this lethal deletion (10.8%) likely results from its strong positive association with growth rate in heterozygous individuals, an important selection trait in the pig breeding industry. Interestingly, we show that the positive effect on growth is induced by a heterozygous loss-of-function of the BBS9 gene, associated with obesity in human and mouse. However, late fetal mortality is induced by insufficient expression of the BMPER gene located directly downstream of the deletion which affects its regulatory elements required for gene expression. Together, our study shows an unique example of allelic pleiotropy in which one allele (deletion) is responsible for both increased growth and late fetal mortality by affecting two different genes.

Evolutionary analysis of the carnitine- and choline acyltransferases suggests distinct evolution of CPT2 versus CPT1 and related variants

Carnitine/choline acyltransferases play diverse roles in energy metabolism and neuronal signalling. Our knowledge of their evolutionary relationships, important for functional understanding, is incomplete. Therefore, we aimed to determine the evolutionary relationships of these eukaryotic transferases. We performed extensive phylogenetic and intron position analyses. We found that mammalian intramitochondrial CPT2 is most closely related to cytosolic yeast carnitine transferases (Sc-YAT1 and 2), whereas the other members of the family are related to intraorganellar yeast Sc-CAT2. Therefore, the cytosolically active CPT1 more closely resembles intramitochondrial ancestors than CPT2. The choline acetyltransferase is closely related to carnitine acetyltransferase and shows lower evolutionary rates than long chain acyltransferases. In the CPT1 family several duplications occurred during animal radiation, leading to the isoforms CPT1A, CPT1B and CPT1C. In addition, we found five CPT1-like genes in Caenorhabditis elegans that strongly group to the CPT1 family. The long branch leading to mammalian brain isoform CPT1C suggests that either strong positive or relaxed evolution has taken place on this node. The presented evolutionary delineation of carnitine/choline acyltransferases adds to current knowledge on their functions and provides tangible leads for further experimental research.

A plug and produce framework for industrial collaborative robots

Collaborative robots are today ever more interesting in response to the increasing need for agile manufacturing equipment. Contrary to traditional industrial robots, collaborative robots are intended for working in dynamic environments alongside the production staff. To cope with the dynamic environment and workflow, new configuration and control methods are needed compared to those of traditional industrial robots. The new methods should enable shop floor operators to reconfigure the robot. This article presents a plug and produce framework for industrial collaborative robots. The article focuses on the control framework enabling quick and easy exchange of hardware modules as an approach to achieving plug and produce. To solve this, an agent-based system is proposed building on top of the robot operating system. The framework enables robot operating system packages to be adapted into agents and thus supports the software sharing of the robot operating system community. A clear separation of the hardware agents and the higher level task control is achieved through standardization of the functional interface, a standardization maintaining the possibility of specialized function features. A feasibility study demonstrates the validity of the framework through a series of reconfigurations performed on a modular collaborative robot.

Abstract 2426: Oncopig soft-tissue sarcomas recapitulate key transcriptional features of human sarcomas

Human soft-tissue sarcomas (STS) are rare, aggressive mesenchymal tumors with a late stage 5-year survival rate (50-60%) that has for decades remained unchanged. Research into STS treatment is hampered by the limited human STS cell line availability and the large number of STS subtypes. Therefore, there is a need to develop STS cell lines and animal models representative of diverse human STS subtypes. Pigs represent ideal human disease models due to their similar size, anatomy, metabolism, genetics, and epigenetics compared to humans. In this regard, porcine cancer models provide the opportunity to produce STS cell lines and in vivo tumors similar to those clinically observed in humans. The Oncopig encodes Cre recombinase inducible porcine transgenes encoding KRASG12D and TP53R167H, allowing the Oncopig to model a number of human sarcomas in an inducible and temporal manner. However, comparative analysis is required to determine to what extend the Oncopig STS model mimics human STS on a molecular level. The purpose of this study was to identify similarities between Oncopig and human STS transcriptional profiles to validate the Oncopig model as a viable model for human STS. Towards this end, Oncopig fibroblasts were isolated from ear notches of 4 Oncopigs and cultured in vitro. Following confirmation of their mesenchymal origin (positive vimentin immunostaining), Oncopig fibroblasts were transformed via Cre recombinase exposure, resulting in the formation of Oncopig STS cell lines. Oncopig STS tumors were produced in vivo through intramuscular injection of adenovirus encoding Cre in 2 Oncopigs (2 sites/Oncopig), resulting in the formation of 4 tumors detectable by 10 days post injection. The mesenchymal origin of the resulting tumors was confirmed through histological characterization. Genome-wide expression of Oncopig STS cell lines and tumors was profiled via RNA-seq. Reproducible Oncopig STS cell line and tumor expression profiles were observed, and Oncopig STS cell lines also displayed high temporal reproducibility. Differential expression analysis was performed by comparing Oncopig STS cell lines and tumors to untransformed fibroblasts and skeletal muscle, respectively. A total of 3,360 and 7,652 differentially expressed genes were identified in the Oncopig STS cell lines and tumors, respectively. Commonly identified alterations in human STS gene expression and pathway regulation were identified in Oncopig STS, including altered TP53 signaling, activation of Wnt signaling, and evidence of epigenetic reprogramming. Furthermore, master regulators of Oncopig STS gene expression were identified, including FOSL1, which was previously identified as a potential therapeutic target for human STS. These results demonstrate the Oncopig STS model’s ability to mimic human STS on a transcriptomic level, making the Oncopig a valuable resource for sarcoma research and cell line development.

Citation Format: Kyle M. Schachtschneider, Yingkai Liu, Suvi Makelainen, Ole Madsen, Laurie A. Rund, Martien A. Groenen, Regina M. Schwind, Ron C. Gaba, Schook B. Lawrence. Oncopig soft-tissue sarcomas recapitulate key transcriptional features of human sarcomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2426. doi:10.1158/1538-7445.AM2017-2426

After genome-wide association studies: Gene networks elucidating candidate genes divergences for number of teats across two pig populations

Number of teats (NT) is an important trait affecting both piglet's welfare and the production level of pig farms. Biologically, embryonic mammary gland development requires the coordination of many signaling pathways necessary for the proper development of teats. Several QTL for NT have been identified; however, further analysis is still lacking. Therefore, gene networks derived from genomewide association study (GWAS) results can be used to examine shared pathways and functions of putative candidate genes. Besides, such analyses may also be helpful to understand the genetic diversity between populations for the same trait or traits. In this study, we identified significant SNP for Landrace-based (line C) and Large White-based (line D) dam lines. Besides, gene-transcription factor (TF) networks were constructed aiming to obtain the most likely candidate genes for NT in each line followed by a comparative analysis between both lines to access similarities or dissimilarities at the marker and gene level. We identified 24 and 19 significant SNP (Bayes factor ≥ 100) for lines C and D, respectively. Only 1 significant SNP overlapped both lines. Network analysis illustrated gene interactions consistent with known mammal's breast biology and captured known TF. We observed different sets of putative candidate genes for NT in each line evaluated that may have common effects on the phenotype. Based on these results, we demonstrated the importance of post-GWAS analyses increasing the biological understanding of relevant genes for a complex trait. Moreover, we believe that this genomic diversity across lines should be taken into account, considering breed-specific reference populations for genomic selection.

The Importance of Endophenotypes to Evaluate the Relationship between Genotype and External Phenotype

With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal's transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal's genome and its environment that range from the cellular, up to the husbandry environment. Thus, understanding complex traits requires knowledge about not only genomic variation, but also environmental effects that affect genome expression. Gene products act together in physiological pathways and interaction networks (of pathways). Due to the lack of annotation of the functional genome and ontologies of genes, our knowledge about the various biological systems that contribute to the development of external phenotypes is sparse. Furthermore, interaction with the animals' microbiome, especially in the gut, greatly influences the external phenotype. We conclude that a detailed understanding of complex traits requires not only understanding of variation in the genome, but also its expression at all functional levels.

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs.

Impact of neonatal iron deficiency on hippocampal DNA methylation and gene transcription in a porcine biomedical model of cognitive development

BACKGROUND

Iron deficiency is a common childhood micronutrient deficiency that results in altered hippocampal function and cognitive disorders. However, little is known about the mechanisms through which neonatal iron deficiency results in long lasting alterations in hippocampal gene expression and function. DNA methylation is an epigenetic mark involved in gene regulation and altered by environmental factors. In this study, hippocampal DNA methylation and gene expression were assessed via reduced representation bisulfite sequencing and RNA-seq on samples from a previous study reporting reduced hippocampal-based learning and memory in a porcine biomedical model of neonatal iron deficiency.

RESULTS

In total 192 differentially expressed genes (DEGs) were identified between the iron deficient and control groups. GO term and pathway enrichment analysis identified DEGs associated with hypoxia, angiogenesis, increased blood brain barrier (BBB) permeability, and altered neurodevelopment and function. Of particular interest are genes previously implicated in cognitive deficits and behavioral disorders in humans and mice, including HTR2A, HTR2C, PAK3, PRSS12, and NETO1. Altered genome-wide DNA methylation was observed across 0.5 million CpG and 2.4 million non-CpG sites. In total 853 differentially methylated (DM) CpG and 99 DM non-CpG sites were identified between groups. Samples clustered by group when comparing DM non-CpG sites, suggesting high conservation of non-CpG methylation in response to neonatal environment. In total 12 DM sites were associated with 9 DEGs, including genes involved in angiogenesis, neurodevelopment, and neuronal function.

CONCLUSIONS

Neonatal iron deficiency leads to altered hippocampal DNA methylation and gene regulation involved in hypoxia, angiogenesis, increased BBB permeability, and altered neurodevelopment and function. Together, these results provide new insights into the mechanisms through which neonatal iron deficiency results in long lasting reductions in cognitive development in humans.

Gene and transposable element methylation in great tit (Parus major) brain and blood

BACKGROUND

Studies on vertebrate DNA methylomes have revealed a regulatory role of tissue specific DNA methylation in relation to gene expression. However, it is not well known how tissue-specific methylation varies between different functional and structural components of genes and genomes. Using whole-genome bisulfite sequencing data we here describe both CpG and non-CpG methylation profiles of whole blood and brain tissue in relation to gene features, CpG-islands (CGIs), transposable elements (TE), and their functional roles in an ecological model species, the great tit (Parus major).

RESULTS

We show that hypomethylation at the transcription start site (TSS) is enriched in genes with functional classes that relate directly to processes specific to each tissue type. We find that 6877 (~21 %) of the CGIs are differentially methylated between blood and brain, of which 1186 and 2055 are annotated to promoter and intragenic regions, respectively. We observe that CGI methylation in promoter regions is more conserved between tissues compared to CGI methylation in intra and inter-genic regions. Differentially methylated CGIs in promoter and intragenic regions are overrepresented in genomic loci linked to development, suggesting a distinct role for CGI methylation in regulating expression during development. Additionally, we find significant non-CpG methylation in brain but not in blood with a strong preference for methylation at CpA dinucleotide sites. Finally, CpG hypermethylation of TEs is significantly stronger in brain compared to blood, but does not correlate with TE activity. Surprisingly, TEs showed significant hypomethylation in non-CpG contexts which was negatively correlated with TE expression.

CONCLUSION

The discovery that TSS methylation levels are directly linked to functional classes related to each tissue provides new insights in the regulatory role of DNA-methylation patterns. The dominant sequence motifs for brain non-CpG methylation, similar to those found in mammals, suggests that a conserved non-CpG regulatory mechanism was already present in the amniote ancestor. The negative correlation between brain non-CpG methylation and TE activity (not found for CpG methylation) suggests that non-CpG is the dominant regulatory form of methylation in TE silencing.

Revealing new candidate genes for reproductive traits in pigs: combining Bayesian GWAS and functional pathways

Background

Reproductive traits such as number of stillborn piglets (SB) and number of teats (NT) have been evaluated in many genome-wide association studies (GWAS). Most of these GWAS were performed under the assumption that these traits were normally distributed. However, both SB and NT are discrete (e.g. count) variables. Therefore, it is necessary to test for better fit of other appropriate statistical models based on discrete distributions. In addition, although many GWAS have been performed, the biological meaning of the identified candidate genes, as well as their functional relationships still need to be better understood. Here, we performed and tested a Bayesian treatment of a GWAS model assuming a Poisson distribution for SB and NT in a commercial pig line. To explore the biological role of the genes that underlie SB and NT and identify the most likely candidate genes, we used the most significant single nucleotide polymorphisms (SNPs), to collect related genes and generated gene-transcription factor (TF) networks.

Results

Comparisons of the Poisson and Gaussian distributions showed that the Poisson model was appropriate for SB, while the Gaussian was appropriate for NT. The fitted GWAS models indicated 18 and 65 significant SNPs with one and nine quantitative trait locus (QTL) regions within which 18 and 57 related genes were identified for SB and NT, respectively. Based on the related TF, we selected the most representative TF for each trait and constructed a gene-TF network of gene-gene interactions and identified new candidate genes.

Conclusions

Our comparative analyses showed that the Poisson model presented the best fit for SB. Thus, to increase the accuracy of GWAS, counting models should be considered for this kind of trait. We identified multiple candidate genes (e.g. PTP4A2, NPHP1, and CYP24A1 for SB and YLPM1, SYNDIG1L, TGFB3, and VRTN for NT) and TF (e.g. NF-κB and KLF4 for SB and SOX9 and ELF5 for NT), which were consistent with known newborn survival traits (e.g. congenital heart disease in fetuses and kidney diseases and diabetes in the mother) and mammary gland biology (e.g. mammary gland development and body length).

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0189-x) contains supplementary material, which is available to authorized users.

Evolutionary signals of selection on cognition from the great tit genome and methylome

For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory- and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species.

The great tit (Parus major) is known for its complex social-cognitive behaviour. Here, the authors sequence genomes of the great tit and show genes related to learning and cognition in regions under positive selection, as well as neuronal non-CpG methylation patterns similar to those observed in mammals.

Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model

Background

Pigs (Sus scrofa) provide relevant biomedical models to dissect complex diseases due to their anatomical, genetic, and physiological similarities with humans. Aberrant DNA methylation has been linked to many of these diseases and is associated with gene expression; however, the functional similarities and differences between porcine and human DNA methylation patterns are largely unknown.

Methods

DNA and RNA was isolated from eight tissue samples (fat, heart, kidney, liver, lung, lymph node, muscle, and spleen) from the adult female Duroc utilized for the pig genome sequencing project. Reduced representation bisulfite sequencing (RRBS) and RNA-seq were performed on an Illumina HiSeq2000. RRBS reads were aligned using BSseeker2, and only sites with a minimum depth of 10 reads were used for methylation analysis. RNA-seq reads were aligned using Tophat, and expression analysis was performed using Cufflinks. In addition, SNP calling was performed using GATK for targeted control and whole genome sequencing reads for CpG site validation and allelic expression analysis, respectively.

Results

Analysis on the influence of DNA variation in methylation calling revealed a reduced effectiveness of WGS datasets in covering CpG rich regions, as well as the usefulness of a targeted control library for SNP detection. Analysis of over 500,000 CpG sites demonstrated genome wide methylation patterns similar to those observed in humans, including reduced methylation within CpG islands and at transcription start sites (TSS), X chromosome inactivation, and anticorrelation of TSS CpG methylation with gene expression. In addition, a positive correlation between TSS CpG density and expression, and a negative correlation between TSS TpG density and expression were demonstrated. Low but non-random non-CpG methylation (<1%) was also detected in all non-neuronal somatic tissues, with differences in tissue clustering observed based on CpG and non-CpG methylation patterns. Finally, allele specific expression analysis revealed enrichment of genes involved in metabolic and regulatory processes. 

Discussion

These results provide transcriptional and DNA methylation datasets for the biomedical community that are directly relatable to current genomic resources. In addition, the correlation between TSS CpG density and expression suggests increased mutation rates at CpG sites play a significant role in adaptive evolution by reducing CpG density at TSS over time, resulting in higher methylation levels in these regions and more permanent changes to lower gene expression. This is proposed to occur predominantly through deamination of 5-methylcytosine to thymidine, resulting in the replacement of CpG with TpG sites in these regions, as indicated by the increased TSS TpG density observed in non-expressed genes, resulting in a negative correlation between expression and TSS TpG density.

Conclusions

This study provides baseline methylation and gene transcription profiles for a healthy adult pig, reports similar patterns to those observed in humans, and supports future porcine studies related to human disease and development. Additionally, the observed reduced CpG and increased TpG density at TSS of lowly expressed genes suggests DNA methylation plays a significant role in adaptive evolution through more permanent changes to lower gene expression.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1938-x) contains supplementary material, which is available to authorized users.

Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes

Traditionally, the process of domestication is assumed to be initiated by humans, involve few individuals and rely on reproductive isolation between wild and domestic forms. We analyzed pig domestication using over 100 genome sequences and tested whether pig domestication followed a traditional linear model or a more complex, reticulate model. We found that the assumptions of traditional models, such as reproductive isolation and strong domestication bottlenecks, are incompatible with the genetic data. In addition, our results show that, despite gene flow, the genomes of domestic pigs have strong signatures of selection at loci that affect behavior and morphology. We argue that recurrent selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars and created 'islands of domestication' in the genome. Our results have major ramifications for the understanding of animal domestication and suggest that future studies should employ models that do not assume reproductive isolation.

Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

Conservation and breeding programs aim at maintaining the most diversity, thereby avoiding deleterious effects of inbreeding while maintaining enough variation from which traits of interest can be selected. Theoretically, the most diversity is maintained using optimal contributions based on many markers to calculate coancestries, but this can decrease fitness by maintaining linked deleterious variants. The heterogeneous patterns of coancestry displayed in pigs make them an excellent model to test these predictions. We propose methods to measure coancestry and fitness from resequencing data and use them in population management. We analyzed the resequencing data of Sus cebifrons, a highly endangered porcine species from the Philippines, and genotype data from the Pietrain domestic breed. By analyzing the demographic history of Sus cebifrons, we inferred two past bottlenecks that resulted in some inbreeding load. In Pietrain, we analyzed signatures of selection possibly associated with commercial traits. We also simulated the management of each population to assess the performance of different optimal contribution methods to maintain diversity, fitness, and selection signatures. Maximum genetic diversity was maintained using marker-by-marker coancestry, and least using genealogical coancestry. Using a measure of coancestry based on shared segments of the genome achieved the best results in terms of diversity and fitness. However, this segment-based management eliminated signatures of selection. We demonstrate that maintaining both diversity and fitness depends on the genomic distribution of deleterious variants, which is shaped by demographic and selection histories. Our findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programs.

Copy number variation in the speciation of pigs: a possible prominent role for olfactory receptors

Background

Unraveling the genetic mechanisms associated with reduced gene flow between genetically differentiated populations is key to understand speciation. Different types of structural variations (SVs) have been found as a source of genetic diversity in a wide range of species. Previous studies provided detailed knowledge on the potential evolutionary role of SVs, especially copy number variations (CNVs), between well diverged species of e.g. primates. However, our understanding of their significance during ongoing speciation processes is limited due to the lack of CNV data from closely related species. The genus Sus (pig and its close relatives) which started to diverge ~4 Mya presents an excellent model for studying the role of CNVs during ongoing speciation.

Results

In this study, we identified 1408 CNV regions (CNVRs) across the genus Sus. These CNVRs encompass 624 genes and were found to evolve ~2.5 times faster than single nucleotide polymorphisms (SNPs). The majority of these copy number variable genes are olfactory receptors (ORs) known to play a prominent role in food foraging and mate recognition in Sus. Phylogenetic analyses, including novel Bayesian analysis, based on CNVRs that overlap ORs retain the well-accepted topology of the genus Sus whereas CNVRs overlapping genes other than ORs show evidence for random drift and/or admixture.

Conclusion

We hypothesize that inter-specific variation in copy number of ORs provided the means for rapid adaptation to different environments during the diversification of the genus Sus in the Pliocene. Furthermore, these regions might have acted as barriers preventing massive gene flow between these species during the multiple hybridization events that took place later in the Pleistocene suggesting a possible prominent role of ORs in the ongoing Sus speciation.

Electronic supplementary material

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Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Background

Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog.

Results

Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal.

Conclusions

Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.