Calculating Volume of Pig Point Cloud Based on Improved Poisson Reconstruction

Pig point cloud data can be used to digitally reconstruct surface features, calculate pig body volume and estimate pig body weight. Volume, as a pig novel phenotype feature, has the following functions: (a) It can be used to estimate livestock weight based on its high correlation with body weight. (b) The volume proportion of various body parts (such as head, legs, etc.) can be obtained through point cloud segmentation, and the new phenotype information can be utilized for breeding pigs with smaller head volumes and stouter legs. However, as the pig point cloud has an irregular shape and may be partially missing, it is difficult to form a closed loop surface for volume calculation. Considering the better water tightness of Poisson reconstruction, this article adopts an improved Poisson reconstruction algorithm to reconstruct pig body point clouds, making the reconstruction results smoother, more continuous, and more complete. In the present study, standard shape point clouds, a known-volume Stanford rabbit standard model, a measured volume piglet model, and 479 sets of pig point cloud data with known body weight were adopted to confirm the accuracy and reliability of the improved Poisson reconstruction and volume calculation algorithm. Among them, the relative error was 4% in the piglet model volume result. The average absolute error was 2.664 kg in the weight estimation obtained from pig volume by collecting pig point clouds, and the average relative error was 2.478%. Concurrently, it was determined that the correlation coefficient between pig body volume and pig body weight was 0.95.

RASGRP1 targeted by H3K27me3 regulates myoblast proliferation and differentiation in mice and pigs

Skeletal muscle is not only the largest organ in the body that is responsible for locomotion and exercise but also crucial for maintaining the body's energy metabolism and endocrine secretion. The trimethylation of histone H3 lysine 27 (H3K27me3) is one of the most important histone modifications that participates in muscle development regulation by repressing the transcription of genes. Previous studies indicate that the RASGRP1 gene is regulated by H3K27me3 in embryonic muscle development in pigs, but its function and regulatory role in myogenesis are still unclear. In this study, we verify the crucial role of H3K27me3 in RASGRP1 regulation. The gain/loss function of RASGRP1 in myogenesis regulation is performed using mouse myoblast C2C12 cells and primarily isolated porcine skeletal muscle satellite cells (PSCs). The results of qPCR, western blot analysis, EdU staining, CCK-8 assay and immunofluorescence staining show that overexpression of RASGRP1 promotes cell proliferation and differentiation in both skeletal muscle cell models, while knockdown of RASGRP1 leads to the opposite results. These findings indicate that RASGRP1 plays an important regulatory role in myogenesis in both mice and pigs.

DIA-based quantitative proteomic analysis of porcine endometrium in the peri-implantation phase

The 12th day of gestation is a critical period for embryo loss and the beginning of imminent implantation in sows. Data independent acquisition (DIA) technology is one of the high-throughput, high-resolution and reproducible proteomics technologies for large-scale digital qualitative and quantitative research. The aim of this study was to identify and characterize the protein abundance landscape of Yorkshire pig endometrium on the 12th day of pregnancy (P12) and estrous cycle (C12) using DIA proteomics. A total of 1251 differentially abundant proteins (DAPs) were identified, of which 882 were up-regulated and 369 were down-regulated at P12. Functional enrichment analysis showed that the identified proteins were related to metabolism, biosynthesis and signaling pathways. Three proteins were selected for Western blot (WB) validation and the results were consistent with the DIA data. Further combined with transcriptome data, fibrinogen like 2 (FGL2) and S100 calcium binding protein A8 (S100A8) were verified to be highly abundant in the P12 endometrial epithelium. In summary, there were significantly different abundance of proteome profiles in C12 and P12 endometrium, suggesting that DAPs are associated with changes in endometrial receptivity, which laid the foundation for further research on related regulatory mechanisms. SIGNIFICANCE: The 12th day of gestation is an important point in the peri-implantation period of pigs, when the endometrium presents a receptive state under the stimulation of estrogen. DIA proteomics technology is an emerging protein identification technology in recent years, which can obtain protein information through comprehensive and unbiased scanning. In this study, DIA technology was used to characterize endometrial proteins in pigs during the peri-implantation period. The results showed that higher protein abundance was detected using the DIA technique, and some of these DAPs may be involved in regulating embryo implantation. This study will help to better reveal the related proteins involved in embryo implantation, and lay a foundation for further research on the mechanism of endometrial regulation of embryo implantation. SIGNIFICANCE OF THE STUDY: The 12th day of gestation is an important point in the peri-implantation period of pigs, when the endometrium presents a receptive state under the stimulation of estrogen. DIA proteomics technology is an emerging protein identification technology in recent years, which can obtain protein information through comprehensive and unbiased scanning. In this study, DIA technology was used to characterize endometrial proteins in pigs during the peri-implantation period. The results showed that higher protein abundance was detected using the DIA technique, and some of these DAPs may be involved in regulating embryo implantation. This study will help to better reveal the related proteins involved in embryo implantation, and lay a foundation for further research on the mechanism of endometrial regulation of embryo implantation.

Protein Dynamic Landscape of Pig Embryos during Peri-Implantation Development

Properly developed embryos are critical for successful embryo implantation. The dynamic landscape of proteins as executors of biological processes in pig peri-implantation embryos has not been reported so far. In this study, we collected pig embryos from days 9, 12, and 15 of pregnancy during the peri-implantation stage for a PASEF-based quantitative proteomic analysis. In total, approximately 8000 proteins were identified. These proteins were classified as stage-exclusive proteins and stage-specific proteins, respectively, based on their presence and dynamic abundance changes at each stage. Functional analysis showed that their roles are consistent with the physiological processes of corresponding stages, such as the biosynthesis of amino acids and peptides at P09, the regulation of actin cytoskeletal organization and complement activation at P12, and the vesicular transport at P15. Correlation analysis between mRNAs and proteins showed a general positive correlation between pig peri-implantation embryonic mRNAs and proteins. Cross-species comparisons with human early embryos identified some conserved proteins that may be important in regulating embryonic development, such as STAT3, AP2A1, and PFAS. Our study provides a comprehensive overview of the pig embryo proteome during implantation, fills gaps in relevant developmental studies, and identifies some important proteins that may serve as potential targets for future research.

Genomic prediction based on preselected single-nucleotide polymorphisms from genome-wide association study and imputed whole-genome sequence data annotation for growth traits in Duroc pigs

The use of whole-genome sequence (WGS) data is expected to improve genomic prediction (GP) power of complex traits because it may contain mutations that in strong linkage disequilibrium pattern with causal mutations. However, a few previous studies have shown no or small improvement in prediction accuracy using WGS data. Incorporating prior biological information into GP seems to be an attractive strategy that might improve prediction accuracy. In this study, a total of 6334 pigs were genotyped using 50K chips and subsequently imputed to the WGS level. This cohort includes two prior discovery populations that comprise 294 Landrace pigs and 186 Duroc pigs, as well as two validation populations that consist of 3770 American Duroc pigs and 2084 Canadian Duroc pigs. Then we used annotation information and genome-wide association study (GWAS) from the WGS data to make GP for six growth traits in two Duroc pig populations. Based on variant annotation, we partitioned different genomic classes, such as intron, intergenic, and untranslated regions, for imputed WGS data. Based on GWAS results of WGS data, we obtained trait-associated single-nucleotide polymorphisms (SNPs). We then applied the genomic feature best linear unbiased prediction (GFBLUP) and genomic best linear unbiased prediction (GBLUP) models to estimate the genomic estimated breeding values for growth traits with these different variant panels, including six genomic classes and trait-associated SNPs. Compared with 50K chip data, GBLUP with imputed WGS data had no increase in prediction accuracy. Using only annotations resulted in no increase in prediction accuracy compared to GBLUP with 50K, but adding annotation information into the GFBLUP model with imputed WGS data could improve the prediction accuracy with increases of 0.00%-2.82%. In conclusion, a GFBLUP model that incorporated prior biological information might increase the advantage of using imputed WGS data for GP.

New olive-pomace fertilizer tested with a 2-tiers approach: Biomarkers on Eisenia fetida, physiochemical effects on Solanum lycopersicum and Olea europaea

Every year, the olive oil industry generates a substantial amount of pomace, a semi-solid residue made up of skin, pulp, pit, and kernel fragments. Rather than being disposed of, the pomace can be dried and transported to an extraction facility where pomace oil can be extracted. Utilizing its high thermal capacity, the extracted pomace can be used as a supplementary fuel in the drying process, resulting in the production of ashes. In this study, the effect of pomace waste applied to the soil was investigated by testing two mixtures with different proportions of de-oiled pomace flour and kernel ash (50:50 and 70:30, respectively) in powder and pellet form. We used a dual approach, evaluating the effects of the mixtures on both soil communities and plant physiology and productivity, to assess the actual usability of the fertilizer in agriculture. The biomarker approach was valuable in assessing the sublethal effects of the two mixtures in powder form in soil. After 30 days of exposure, the bioindicator organism Eisena fetida showed lipid peroxidation, glutathione S-transferase and lactate dehydrogenase levels similar to the control, while lysozyme activity was reduced in all treatments. The powder mixture was lethal to the tomato plants, while there was no evidence of any damage to the olive trees. During 60 days of monitoring, both mixtures in pellet form showed a slight increase in physiological parameters, suggesting a benefit to the photosynthetic system. The improved carbon assimilation in tomato plants treated with the mixtures results in increased plant productivity, both in terms of number and weight of fruits, while maintaining the antioxidant content. This study paves the way for the use of the pomace mixture as a soil improver, thus increasing the value of this waste product.

Genome-wide association studies for loin muscle area, loin muscle depth and backfat thickness in DLY pigs

This study aimed at identifying genes associated with loin muscle area (LMA), loin muscle depth (LMD) and backfat thickness (BFT). We performed single-trait and multi-trait genome-wide association studies (GWASs) after genotyping 685 Duroc × (Landrace × Yorkshire) (DLY) pigs using the Geneseek Porcine 50K SNP chip. In the single-trait GWASs, we identified two, eight and two significant SNPs associated with LMA, LMD and BFT, respectively, and searched genes within the 1 Mb region near the significant SNPs with relevant functions as candidate genes. Consequently, we identified one (DOCK5), three (PID1, PITX2, ELOVL6) and three (CCR1, PARP14, CASR) promising candidate genes for LMA, LMD and BFT, respectively. Moreover, the multi-trait GWAS identified four significant SNPs associated with the three traits. In conclusion, the GWAS analysis of LMA, LMD and BFT in a DLY pig population identified several associated SNPs and candidate genes, further deepening our understanding of the genetic basis of these traits, and they may be useful for marker-assisted selection to improve the three traits in DLY pigs.

The effects of boar seminal plasma extracellular vesicles on sperm fertility

Extracellular vesicles (EVs) are abundant in body fluid and are critical in cell interaction. Seminal plasma contains numerous EVs which affecting sperm function via transferring regulatory cargoes to the sperm. However, the mechanism of seminal plasma extracellular vesicles (SP-EVs) is still not clear. The present study aimed to isolate the boar SP-EVs and explore its potential function, then identify the key protein involved in SP-EVs and sperms interaction, and elucidate mechanism of SP-EVs protein on sperms. Here, we successfully isolated and concentrated boar SP-EVs, the SP-EVs showed a typical vesicle structure under transmission electron microscopy, most of their diameters range between 50 and 200 nm and express EVs biomarkers CD9 and CD63. We proved that SP-EVs could inhibit sperm acrosome reaction and in vitro fertility. Through a data-independent acquisition analysis of protein profiles of noncapacitated sperms, normal capacitated sperms and SP-EVs treated capacitated sperms, we identified that EZRIN was one of the active proteins that participated in SP-EVs and sperms interaction. Furthermore, we tested that the inhibition of EZRIN could promote boar sperm fertility, which is in consistence with the function of SP-EVs. The results may facilitate future research of SP-EVs on sperm function and male infertility.

The global burden of lymphoma: estimates from the Global Burden of Disease 2019 study

OBJECTIVES

The aim of this study was to describe the global trends in the burden of lymphoma from 1990 to 2019.

STUDY DESIGN

The data used in this study were from the Global Burden of Disease 2019 study.

METHODS

This study described the age-standardised rates of incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life years (DALYs) of lymphoma (non-Hodgkin and Hodgkin's lymphoma, NHL and HL, respectively) annually from 1990 to 2019, stratified by sociodemographic index (SDI) and 21 world regions. The estimated annual percentage changes in these indexes were calculated.

RESULTS

In 2019, the age-standardised rates of HL per 100,000 population were lower than those of NHL in terms of incidence (1.1 vs 6.7 per 100,000 person-years, respectively) and prevalence (0.3 vs 5.7 per 100,000 person-years, respectively) but not mortality (21.6 vs 3.2 per 100,000 person-years, respectively). From 1999 to 2019, the global incidence of HL decreased and the incidence of NHL increased, and the prevalence of both HL and NHL increased, but the mortality rates decreased. When stratified by SDI, the incidence of HL decreased in all but middle-SDI regions, the mortality rate of HL decreased in all regions, and both the incidence and mortality rate of NHL increased in all but high-SDI regions. The prevalence of HL and NHL increased in all SDI regions, especially in middle-SDI regions. YLLs and DALYs of HL in all SDI regions and those of NHL in high-SDI regions decreased. YLDs slightly increased in middle- to high-SDI regions.

CONCLUSIONS

Lymphoma remains a major public health issue, and better prevention, precise identification, and promising treatments are vitally important.

Genome-Wide Association Study for Somatic Skeletal Traits in Duroc × (Landrace × Yorkshire) Pigs

The pig bone weight trait holds significant economic importance in southern China. To expedite the selection of the pig bone weight trait in pig breeding, we conducted molecular genetic research on these specific traits. These traits encompass the bone weight of the scapula (SW), front leg bone weight (including humerus and ulna) (FLBW), hind leg bone weight (including femur and tibia) (HLBW), and spine bone weight (SBW). Up until now, the genetic structure related to these traits has not been thoroughly explored, primarily due to challenges associated with obtaining the phenotype data. In this study, we utilized genome-wide association studies (GWAS) to discern single nucleotide polymorphisms (SNPs) and genes associated with four bone weight traits within a population comprising 571 Duroc × (Landrace × Yorkshire) hybrid pigs (DLY). In the analyses, we employed a mixed linear model, and for the correction of multiple tests, both the false discovery rate and Bonferroni methods were utilized. Following functional annotation, candidate genes were identified based on their proximity to the candidate sites and their association with the bone weight traits. This study represents the inaugural application of GWAS for the identification of SNPs associated with individual bone weight in DLY pigs. Our analysis unveiled 26 SNPs and identified 12 promising candidate genes (OPRM1, SLC44A5, WASHC4, NOPCHAP1, RHOT1, GLP1R, TGFB3, PLCB1, TLR4, KCNJ2, ABCA6, and ABCA9) associated with the four bone weight traits. Furthermore, our findings on the genetic mechanisms influencing pig bone weight offer valuable insights as a reference for the genetic enhancement of pig bone traits.

Genetic evaluation for production and body size traits using different animal models in purebred-Duroc pigs

Duroc pigs are popular crossbred terminal sires, and accurate assessment of genetic parameters in the population can help to rationalize breeding programmes. The principle aim of this study were to evaluate the genetic parameters of production (birth weight, BW; age at 115 kg, AGE; feed conversion ratio, FCR) and body size (body length, BL; body height, BH; front cannon circumference, FCC) traits of Duroc pigs. The second objective was to analyze the fit of different genetic assessment models. The variance components and correlations of BW (28,348 records), AGE (28,335 records), FCR (11,135 records), BL (31,544 records), BH (21,862 records), and FCC (14,684 records) traits were calculated by using DMU and AIREMLF90 from BLUPF90 package. In the common environment model, the heritability of BW, AGE, FCR, BL, BH, and FCC traits were 0.17 ± 0.014, 0.30 ± 0.019, 0.28 ± 0.024, 0.16 ± 0.013, 0.14 ± 0.017, and 0.081 ± 0.016, with common litter effect values of 0.25, 0.20, 0.18, 0.23, 0.19, and 0.16, respectively. According to the results of the Akaike information criterion (AIC) calculations, models with smaller AIC values have a better fit. We found that the common environment model with litter effects as random effects for estimating genetic parameters had a better fit. In this Model, the estimated genetic correlations between AGE with BW, FCR, BL, BH, and FCC traits were -0.28 (0.040), 0.76 (0.038), -0.71 (0.036), -0.44 (0.060), and -0.60 (0.073), respectively, with phenotypic correlations of -0.17, 0.52, -0.22, -0.13 and -0.24, respectively. In our analysis of genetic trends for six traits in the Duroc population from 2012 to 2021, we observed significant genetic trends for AGE, BL, and BH. Particularly noteworthy is the rapid decline in the genetic trend for AGE, indicating an enhancement in the pig's growth rate through selective breeding. Therefore, we believe that some challenging-to-select traits can benefit from the genetic correlations between traits. By selecting easily measurable traits, they can gain from synergistic selection effects, leading to genetic progress. Conducting population genetic parameter analysis can assist us in devising breeding strategies.

Increased Accuracy of Genomic Prediction Using Preselected SNPs from GWAS with Imputed Whole-Genome Sequence Data in Pigs

Enhancing the accuracy of genomic prediction is a key goal in genomic selection (GS) research. Integrating prior biological information into GS methods using appropriate models can improve prediction accuracy for complex traits. Genome-wide association study (GWAS) is widely utilized to identify potential candidate loci associated with complex traits in livestock and poultry, offering essential genomic insights. In this study, a GWAS was conducted on 685 Duroc × Landrace × Yorkshire (DLY) pigs to extract significant single-nucleotide polymorphisms (SNPs) as genomic features. We compared two GS models, genomic best linear unbiased prediction (GBLUP) and genomic feature BLUP (GFBLUP), by using imputed whole-genome sequencing (WGS) data on 651 Yorkshire pigs. The results revealed that the GBLUP model achieved prediction accuracies of 0.499 for backfat thickness (BFT) and 0.423 for loin muscle area (LMA). By applying the GFBLUP model with GWAS-based SNP preselection, the average prediction accuracies for BFT and LMA traits reached 0.491 and 0.440, respectively. Specifically, the GFBLUP model displayed a 4.8% enhancement in predicting LMA compared to the GBLUP model. These findings suggest that, in certain scenarios, the GFBLUP model may offer superior genomic prediction accuracy when compared to the GBLUP model, underscoring the potential value of incorporating genomic features to refine GS models.

Genome-wide association analysis unveils candidate genes and loci associated with aplasia cutis congenita in pigs

BACKGROUND

Aplasia cutis congenita (ACC) is a rare genetic disorder characterized by the localized or widespread absence of skin in humans and animals. Individuals with ACC may experience developmental abnormalities in the skeletal and muscular systems, as well as potential complications. Localized and isolated cases of ACC can be treated through surgical and medical interventions, while extensive cases of ACC may result in neonatal mortality. The presence of ACC in pigs has implications for animal welfare. It contributes to an elevated mortality rate among piglets at birth, leading to substantial economic losses in the pig farming industry. In order to elucidate candidate genetic loci associated with ACC, we performed a Genome-Wide Association Study analysis on 216 Duroc pigs. The primary goal of this study was to identify candidate genes that associated with ACC.

RESULTS

This study identified nine significant SNPs associated with ACC. Further analysis revealed the presence of two quantitative trait loci, 483 kb (5:18,196,971-18,680,098) on SSC 5 and 159 kb (13:20,713,440-207294431 bp) on SSC13. By annotating candidate genes within a 1 Mb region surrounding the significant SNPs, a total of 11 candidate genes were identified on SSC5 and SSC13, including KRT71, KRT1, KRT4, ITGB7, CSAD, RARG, SP7, PFKL, TRPM2, SUMO3, and TSPEAR.

CONCLUSIONS

The results of this study further elucidate the potential mechanisms underlying and genetic architecture of ACC and identify reliable candidate genes. These results lay the foundation for treating and understanding ACC in humans.

Composition, function, and timing: exploring the early-life gut microbiota in piglets for probiotic interventions

BACKGROUND

The establishment of a robust gut microbiota in piglets during their early developmental stage holds the potential for long-term advantageous effects. However, the optimal timeframe for introducing probiotics to achieve this outcome remains uncertain.

RESULTS

In the context of this investigation, we conducted a longitudinal assessment of the fecal microbiota of 63 piglets at three distinct pre-weaning time points. Simultaneously, we gathered vaginal and fecal samples from 23 sows. Employing 16S rRNA gene and metagenomic sequencing methodologies, we conducted a comprehensive analysis of the fluctuation patterns in microbial composition, functional capacity, interaction networks, and colonization resistance within the gut microbiota of piglets. As the piglets progressed in age, discernible modifications in intestinal microbial diversity, composition, and function were observed. A source-tracking analysis unveiled the pivotal role of fecal and vaginal microbiota derived from sows in populating the gut microbiota of neonatal piglets. By D21, the microbial interaction network displayed a more concise and efficient configuration, accompanied by enhanced colonization resistance relative to the other two time points. Moreover, we identified three strains of Ruminococcus sp. at D10 as potential candidates for improving piglets' weight gain during the weaning phase.

CONCLUSIONS

The findings of this study propose that D10 represents the most opportune juncture for the introduction of external probiotic interventions during the early stages of piglet development. This investigation augments our comprehension of the microbiota dynamics in early-life of piglets and offers valuable insights for guiding forthcoming probiotic interventions.

Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population

BACKGROUND

Although the accumulation of whole-genome sequencing (WGS) data has accelerated the identification of mutations underlying complex traits, its impact on the accuracy of genomic predictions is limited. Reliable genotyping data and pre-selected beneficial loci can be used to improve prediction accuracy. Previously, we reported a low-coverage sequencing genotyping method that yielded 11.3 million highly accurate single-nucleotide polymorphisms (SNPs) in pigs. Here, we introduce a method termed selective linkage disequilibrium pruning (SLDP), which refines the set of SNPs that show a large gain during prediction of complex traits using whole-genome SNP data.

RESULTS

We used the SLDP method to identify and select markers among millions of SNPs based on genome-wide association study (GWAS) prior information. We evaluated the performance of SLDP with respect to three real traits and six simulated traits with varying genetic architectures using two representative models (genomic best linear unbiased prediction and BayesR) on samples from 3579 Duroc boars. SLDP was determined by testing 180 combinations of two core parameters (GWAS P-value thresholds and linkage disequilibrium r2). The parameters for each trait were optimized in the training population by five fold cross-validation and then tested in the validation population. Similar to previous GWAS prior-based methods, the performance of SLDP was mainly affected by the genetic architecture of the traits analyzed. Specifically, SLDP performed better for traits controlled by major quantitative trait loci (QTL) or a small number of quantitative trait nucleotides (QTN). Compared with two commercial SNP chips, genotyping-by-sequencing data, and an unselected whole-genome SNP panel, the SLDP strategy led to significant improvements in prediction accuracy, which ranged from 0.84 to 3.22% for real traits controlled by major or moderate QTL and from 1.23 to 11.47% for simulated traits controlled by a small number of QTN.

CONCLUSIONS

The SLDP marker selection method can be incorporated into mainstream prediction models to yield accuracy improvements for traits with a relatively simple genetic architecture, however, it has no significant advantage for traits not controlled by major QTL. The main factors that affect its performance are the genetic architecture of traits and the reliability of GWAS prior information. Our findings can facilitate the application of WGS-based genomic selection.

Identification of Candidate Genes for Economically Important Carcass Cutting in Commercial Pigs through GWAS

During the process of pork production, the carcasses of pigs are divided and sold, which provides better economic benefits and market competitiveness for pork production than selling the carcass as a whole. Due to the significant cost of post-slaughter phenotypic measurement, the genetic architecture of tenderloin weight (TLNW) and rib weight (RIBW)-important components of pig carcass economic value-remain unknown. In this study, we conducted genome-wide association studies (GWAS) for TLNW and RIBW traits in a population of 431 Duroc × Landrace × Yorkshire (DLY) pigs. In our study, the most significant single nucleotide polymorphism (SNP) associated with TLNW was identified as ASGA0085853 (3.28 Mb) on Sus scrofa chromosome 12 (SSC12), while for RIBW, it was Affx-1115046258 (172.45 Mb) on SSC13. Through haplotype block analysis, we discovered a novel quantitative trait locus (QTL) associated with TLNW, spanning a 5 kb region on SSC12, and a novel RIBW-associated QTL spanning 1.42 Mb on SSC13. Furthermore, we hypothesized that three candidate genes, TIMP2 and EML1, and SMN1, are associated with TLNW and RIBW, respectively. Our research not only addresses the knowledge gap regarding TLNW, but also serves as a valuable reference for studying RIBW. The identified SNP loci strongly associated with TLNW and RIBW may prove useful for marker-assisted selection in pig breeding programs.

Prognostic and Predictive Significance of Tumor Immune Microenvironment in Breast Ductal Carcinoma In Situ

PURPOSE/OBJECTIVE(S)

This study aims to identify the role of different subtypes of tumor infiltrating lymphocytes (TILs) in ductal carcinoma in situ (DCIS) in predicting risk of recurrence and benefit of whole breast irradiation (WBI).

MATERIALS/METHODS

Immunohistochemical stain for CD3, CD4, CD8, FOXP3 and CD20 were carried in a well characterized DCIS cohort who received breast-conserving surgery (BCS) from Jan 2009 to Dec 2018. All the TILs subtypes were evaluated by the average numbers of touching-TILs which defined as TILs touching or within one lymphocyte cell thickness from the malignant ducts' basement membrane. The optimal cut-off values of TILs subtypes were selected by the X-tile.

RESULTS

In total, 167 patients were enrolled in this analysis with 114 patients received WBI. After a median follow-up of 67 months, 15 IBTR events occurred with 6 invasive-IBTRs. Nine out of 15 IBTRs occurred outside of the original quadrant (elsewhere failure event, EFE). CD3+ lymphocytes were the predominant cell subtype while Treg showed the lowest levels. High abundance of TILs subtypes was associated with high tumor grade, presence of microinvasion, high Ki67 index, ER negativity and HER2 positivity. For various TILs subtypes, the multivariate analyses showed that dense CD4+ TILs (HR = 9.84, 95% CI 2.43-39.91, p<0.01) and dense Treg (HR = 4.22, 95% CI 1.24-14.36, p = 0.02) were independent prognostic factors for higher IBTR. As the infiltration of TIL subsets was correlated with one another, we also analyzed the relationship between IBTR and the ratios of different TILs subtypes. By adjusted by clinicopathological parameters, high ratios of CD4+/CD8+, Treg/CD4+ and Treg/CD8+ were found to be independent prognostic factors for higher IBTR (HR = 11.31, 95% CI 3.14-40.76, p<0.01; HR = 3.09, 95% CI 1.05-9.11, p = 0.04; HR = 7.14, 95% CI 1.98-25.73, p<0.01). Consistent with the results of IBTR, the 5-y rate of invasive-IBTR and EFE was both significantly associated with the high CD4+/CD8+, Treg/CD4+ and Treg/CD8+ TILs ratios (all p<0.01). WBI reduced the rate of 5y-IBTR risk from 8.4% to 1.3% (p = 0.02) in the low Treg/CD8+ group, but there was no benefit of WBI in the high group. With respect to EFE, WBI significantly reduced the rate from 2.8% to 0.0% (p = 0.03) in the low Treg/CD8+ group while not in the high group. The benefits of WBI in reducing IBTR and EFE were not significant difference between different CD4+/CD8+ and Treg/CD4+ groups.

CONCLUSION

Assessment of overall TILs provides a tool for comprehensive evaluation of the DCIS immune microenvironment. Patients with pro-tumoral immune infiltrate (high Treg, high ratios of CD4+/CD8+, Treg/CD4+ and Treg/CD8+) in tumor microenvironment show an increased risk of IBTR and less benefit from breast radiotherapy.

TFAM Modulates Cardiomyocytes Pyroptosis Induced by Ionizing Radiation through mtDNA/TLR9/NF-kB Pathway

PURPOSE/OBJECTIVE(S)

Mitochondrial transcription factor A (TFAM) is a pivotal factor for regulating mitochondrial DNA (mtDNA) replication, transcription and biogenesis. Previous studies have reported that cytosolic mtDNA stress can lead to cardiomyocytes pyroptosis, which is characterized by inflammasome formation. In this study, we attempted to investigate the mechanism of TFAM regulate cardiomyocytes pyroptosis induced by ionizing radiation.

MATERIALS/METHODS

The peripheral blood serum of patients with esophageal cancer before and after definitive chemoradiotherapy was collected for Luminex multiplex cytokine assays. C57BL/6 mice were irradiated with the whole heart using small animal radiation research platform (SARRP) to construct a radiation-induced myocardial damage (RIMD) mouse model, and the ventricular function was evaluated using 9.4T Bruker magnetic resonance (MR) scanner. The function changes of cardiomyocytes exposed to radiation were observed in vitro and in vivo after knocking out GSDMD. Furthermore, the changes of mitochondrial function, the levels of cytosolic mtDNA, and the protein levels of NF-kB and pyroptosis pathway in irradiated cardiomyocytes were analyzed by knockdown and overexpression of TFAM in vitro and in vivo.

RESULTS

By multifactor cytokine assays we found that pyroptosis related IL-1β and IL-18 were significantly increased in patients with high mean heart dose (MHD) after radiotherapy, while those with low MHD were not significantly increased after radiotherapy. Next, we successfully constructed the RIMD mouse model using a single heart irradiation of 20 Gy. We found that the gene expression of pyroptosis pathway was significantly up-regulated after cardiac irradiation by myocardial tissue transcriptomic sequencing. Compared with wild-type (WT) mice, cardiac systolic function of Gsdmd-/- mice was significantly improved at 1, 2, 6, 12, and 24 weeks after heart irradiation. In vitro, we also demonstrated increased viability of irradiated cardiomyocytes by knocking out GSDMD. In vitro and in vivo experiments confirmed the expression of TFAM decreased after radiation. By overexpression of TFAM, we found that irradiated cardiomyocytes showed improved mitochondrial function, decreased release of mtDNA into cytoplasm through mitochondrial permeability transition pores (mPTPs), decreased binding of cytosolic mtDNA to TLR9, and decreased expression of NF-kB and pyroptosis pathway proteins. Dual luciferase gene reporter assays and Chromatin immunoprecipitation (CHIP) assay confirmed that p65 could bind the NLRP3 promoter region. In addition, we found that ventricular function deteriorated and improved in mice with knockdown and overexpression of TFAM through adeno-associated virus serotype 9 (AAV9), respectively.

CONCLUSION

Our study indicated that TFAM regulate irradiated cardiomyocytes pyroptosis through mtDNA/TLR9/NF-kB pathway. We provide a novel mechanism of RIMD, revealing an underappreciated intervention target for RIMD.

Quality Assurance of Protocol Compliance in a Multicenter Randomized Trial Investigating the Role of Hypofractionated Comprehensive Reginal Nodal Irradiation in Node-Positive Breast Cancer (HARVEST)

PURPOSE/OBJECTIVE(S)

The HARVEST trial (NCT03829553) is a phase III, multicenter, randomized clinical trial to explore efficacy and safety of hypofractionated irradiation (HFI) involving regional nodal irradiation (RNI, including internal mammary nodes, IMN) in N+ breast cancer patients treated with mastectomy or breast conserving surgery (BCS). Current study aims to analyze the dosimetric quality assurance so as to evaluate the compliance to the trial protocol.

MATERIALS/METHODS

Eligible patients were randomly assigned (1:1) to receive conventional fractionated irradiation (CFI: 50 Gy/25Fx) or HFI (40.05 Gy/15Fx), which is delivered to ipsilateral chest wall or whole breast (CW/WB) with tumor bed boost (HFI: 10.68 Gy/4Fx; CFI: 10 Gy/5Fx) and comprehensive RNI (supra/infraclavicular nodes and IMN in each patient, lower axilla if indicated) by using IMRT technique. The plan quality was evaluated based on dose distribution, dose volume histogram (DVH) and field parameters. The target coverage, including planning target volume of CW/WB (PTV1) and tumor bed (PTV2) and doses of the organs at risk (OARs) were evaluated. The LQ model was used to convert doses of OARs in HFI group using α/β = 3 Gy (EQD23) for comparison.

RESULTS

Between Feb 21, 2019 and Feb 14, 2022, 801 patients were enrolled at 8 centers with 401 and 400 in CFI and HFI group, respectively. There were 182 patients received BCS and 387 patients were with more than three positive lymph nodes. In the CFI group, the D90 and V45 of PTV1 reached the prescribed dose in 70.6% and 96.0% of the patients, respectively. In the HFI group, the D90 and V36 of PTV1 reached the prescribed dose in 87.8% and 95.5% of the patients, respectively. When the tumor bed was irradiated, the D90 of PTV2 reached the prescribed dose in 95.6% in the CFI group and 100% in the HFI group, respectively. The mean D90 of PTV1 and PTV2 were 50.09±0.65 Gy and 60.63±0.91 Gy in CFI group while 40.11±0.56 Gy and 50.79±2.03 Gy in HFI group. For OARs constraints, protocol compliance was all above 95% (heart: 95.3%; ipsilateral lung: 95.5%; contralateral lung: 97.1%; humeral head: 98.2% and spinal cord: 100%) with no significant difference between CFI and HFI groups. For patients with left-sided breast cancer, the Dmean of the heart was 5.10±1.75 Gy vs. 4.59±1.86 Gy (EQD23) in CFI and HFI groups (p = 0.51), respectively. No significant differences in Dmean of the heart (1.45±0.71 Gy vs. 1.33±0.77 Gy (EQD23), p = 0.40) was found either between two groups in right-sided patients. The differences were significant in the Dmean of the ipsilateral lung (13.37±1.99 Gy vs. 11.17±3.50 Gy (EQD23), p<0.01), contralateral lung (0.88±0.73 Gy vs. 0.74±0.61 Gy (EQD23), p<0.01) and the ipsilateral humeral head (15.27±7.62 Gy vs. 13.05±6.19 Gy (EQD23), p<0.01) and the Dmax of spinal cord (21.40±8.82 Gy vs. 19.47±7.99 Gy (EQD23), p = 0.05) between CFI and HFI groups.

CONCLUSION

A high degree of compliance with protocol dose constraints was found for treatment plans in the HARVEST trial and doses to the most of OARs decreased in HFI group.

The Predictive Value of Changes in Basal Myocardial F-18 Fluorodeoxyglucose Uptake for Cardiotoxicity in Locally Advanced Esophageal Cancer Patients Receiving Definitive Radiotherapy

PURPOSE/OBJECTIVE(S)

To investigate the predictive value of changes in myocardial 18F-FDG uptake for major adverse cardiac events (MACEs) in locally advanced esophageal cancer patients receiving definitive radiotherapy.

MATERIALS/METHODS

Between August 2012 and January 2018, 400 patients with stage II-III esophageal cancer receiving definitive radiotherapy at two institutions were divided into the training (n = 240) and external validation cohorts (n = 160). All patients underwent FDG-PET imaging within 1 week before treatment and 3 months after treatment. Myocardium delineation was performed by Carimas software (version 2.10) based on the AHA 17-segment model. When contouring the left ventricle, the myocardium was automatically divided into basal (segments 1-6), middle (segments 7-12), and apical (segments 13-16) regions, and the mean dose and FDG uptake parameters of each region were obtained by Carimas. Our primary endpoint was MACEs. Patient clinicopathologic factors, dosimetric parameters for the whole heart and cardiac substructures, and myocardial changes within the three regions on 18F-FDG PET were utilized to seek the best predictive models for cardiotoxicity. To avoid multicollinearity between dose-volume histogram (DVH) parameters, we selected the variables with the lowest Akaike Information Criterion (AIC) value from the DVH parameters of the same cardiac structure for the actual modeling procedure. Competing risk analysis and Cox regressions analysis were performed. The predictive performance of the models was evaluated using the area under the receiver operating characteristic curve (AUC) and Brier score.

RESULTS

At a median follow-up interval of 78 months, 28 patients (11.7%) developed MACEs. The basal region of the myocardium received the highest radiation dose, followed by the middle and the apex region. The basal myocardial SUVmax and SUVmean significantly increased after radiotherapy while the apical and middle myocardial SUVmax and SUVmean not significantly increased. In univariate analysis, age, pre-existing cardiac disease, changes in pre- and post-treatment basal myocardial SUVmax and SUVmean (∆SUVmax and ∆SUVmean), and dosimetric parameters for MHD, mean LCX, mean LAD, and mean LV dose were associated with an increased hazard of MACEs. Multivariate analysis showed that basal ∆SUVmean retained significance after adjusting for age, pre-existing cardiac disease, and dosimetric parameters for whole heart and cardiac substructures. The AUCs and Brier scores demonstrated favorable predictive accuracies of the model's integrating variables with significant difference in multivariate analysis when predicting MACEs in the training and validation cohorts.

CONCLUSION

∆SUVmean was an independent indicator of MACE in locally advanced esophageal cancer patients receiving definitive radiotherapy. Changes in basal myocardial FDG uptake is a promising biomaker for predicting radiation-induced cardiotoxicity.

Establishing a Risk Stratification Model to Identify Clinically High-Risk N0 Breast Cancer Who Could Benefit from Regional Nodal Irradiation: A Single Institute Analysis

PURPOSE/OBJECTIVE(S)

The adverse clinical features for pN0 BC patients significantly varies and there is no established clinical risk stratification system to identify those "high-risk" pN0 BC patients who might benefit from RNI. The purpose of this real-world study was to investigate the risk factors for developing recurrence among patients with pathological T1-3N0 breast cancer (BC) treated with breast-conserving surgery (BCS) followed by whole breast irradiation alone (WBI) and identify those clinically high-risk BCs who could benefit from regional nodal irradiation (RNI).

MATERIALS/METHODS

Female BC patients treated from 2009 to 2016 were retrospectively reviewed. The disease-free survival (DFS) and overall survival (OS) were estimated by the Kaplan-Meier method, and survival differences were compared with the log-rank test. Univariate and multivariate analysis was performed using Cox logistic regression analysis. An external validation was conducted by using SEER database.

RESULTS

A total of 622 BC patients treated with BCS+WBI alone were included. With a median follow-up of 82 months, the 7-year OS and DFS for the entire cohort was 97% and 91%, respectively. Multivariable Cox analysis indicated that tumor size (p = 0.006), tumor location (p = 0.033), lymphovascular invasion (LVI) status (p = 0.0028) and Ki-67 index (p = 0.051) were independent risk factors for DFS, while only tumor size was the only independent risk factors for OS (p = 0.029). A scoring system was developed using these four factors and the 7-year DFS and OS were 97% and 96% for patients with 0-1 risk factors, 95% and 82% for patients with ≥2 risk factors (p<0.0001 for DFS, and p = 0.0063 for OS). Based on tumor size and tumor location, an external validation by demonstrated that the 7-year OS was 90% and 88% for patients with 0-1 risk factor, which was significantly better than those defined as high-risk BC patients (82%, p<0.0001).

CONCLUSION

By using our institute database, we establish a risk stratification system for identifying sub-group of pN0 BC patients, who are at high risk for developing recurrence. The results of our study support tailored RT decision-making according to individual risks, which needed to be confirmed in further studies.

Treatment Outcomes and Prognostic Factors of Chemotherapy Combined with Radiotherapy for Patients with Stage I-II Nasal-Type Natural Killer/T-Cell Lymphoma

PURPOSE/OBJECTIVE(S)

The purpose of this study was to assess the treatment outcome and the potential prognostic factors for patients with stage I-II nasal ENKTL treated with radiotherapy (RT) combined chemotherapy (CT).

MATERIALS/METHODS

From July, 2005 to January, 2019, 118 eligible patients were retrospective included in the study. Among the 118 patients, 84 were male and 34 were female. The median age was 45 years (range: 14-77 years). According to the Ann Arbor staging system, 66 patients had stage I disease (Primary tumor invasion (PTI) was present in 29 patients), and 52 patients had stage II disease. B symptoms were observed in 61 patients. The Eastern Cooperative Oncology Group (ECOG) performance score was 0 to 1 in 88 patients. Cervical lymph node involvement was observed in 51 patients. The primary lesions were located in the nasal cavity in 92 cases and in the Waldeyer ring in 26 cases. Five patients had received RT followed by CT (RT + CT), 20 patients had received CT followed by RT (CT + RT), 90 patients had received CT followed by RT, again followed by CT (CT+RT+CT), and 3 patients had received concurrent chemoradiotherapy (CRT) (1 patient received CRT + CT, other 2 patients received CT+CRT+CT). Patients were irradiated with a median dose of 50 Gy (range, 24-61.2). All patients received chemotherapy, 91 received non-anthracycline-based chemotherapy, whereas 27 patients received anthracycline-based chemotherapy. The median number of courses of chemotherapy was four (range: 1-10). Patients were scored as having low-risk disease (n = 50), intermediate-risk disease (n = 60) or high-risk disease (n = 8) according to the prognostic index of natural killer cell lymphoma (PINK).

RESULTS

Among the 118 patients, after initial therapy, the complete response (CR) rate was 82.2% (n = 97), and the partial response (PR) rate was 11.0% (n = 13). The stable disease (SD) rate was 2.5% (n = 3), and the progressive disease (PD) rate was 4.2% (n = 5). With a median follow-up of 43 months (range, 4-201) after irradiation, the 3-year PFS and OS were 76.9% and 82.9%, respectively. The 3-year OS rate was 75.0% for RT + CT, 70.0% for CT + RT, 87.1% for CT + RT+ CT, and 50.0% for CRT (P = 0.052). Three-year OS and PFS were 88.6% and 83.4%, respectively, for non-anthracycline-based chemotherapy regimen compared to 61.6% (P = 0.001) and 58.4% (P = 0.003), respectively, for the anthracycline-based chemotherapy regimen. Three-year OS and PFS were 84.0% and 79.0%, respectively, for patients receiving high-dose RT (≥50 Gy, n = 111) compared to 71.4% (P = 0.076) and 71.4% (P = 0.228), respectively, for low-dose RT (<50 Gy, n = 7). In multivariate analysis, adverse factors associated with OS in our study were chemotherapy regimen and response to RT and CT (P = 0.047, <0.001).

CONCLUSION

Radiotherapy combined with chemotherapy reported promising response rate and a favorable survival for patients with stage I-II nasal ENKTL. Anthracycline-based chemotherapy regimen and no remission after RT and CT were adverse factors of OS.

Nodal Response to Neo-Adjuvant Systemic Therapy Predicts Prognosis of cN3c Breast Cancer Patients Receiving Multidisciplinary Therapy

PURPOSE/OBJECTIVE(S)

cN3c breast cancer with ipsilateral supraclavicular (SCV) lymph nodal (SCLN) metastasis has a dismal prognosis. We investigated the survival outcomes, patterns and risks of recurrence in those patients after multidisciplinary therapy, as well as the predictors of candidates for SCV area boosting.

MATERIALS/METHODS

Consecutive cN3c breast cancer patients without distant metastases from January 2009 to December 2020 in our institution were retrospectively reviewed. Based on nodal response to neoadjuvant therapy (NAT), patients were categorized into three groups: clinical complete response (cCR) not achieved in SCLN (Group A, n = 66), SCLN cCR but axillary node (ALN) did not achieve pathological complete response (pCR, Group B, n = 34), cCR in SCLN and pCR in ALN (Group C, n = 13).

RESULTS

The median follow-up time was 32.7 months (range, 21.9-53.3months). The 5-year overall survival (OS) and recurrence-free survival (RFS) rates were 64.6% and 43.7% respectively. Multivariate analysis showed cumulative SCV dose and ypT stage, ALN response and SCV response to NAT were significantly associated with OS and RFS respectively. The 3-year for patients receiving the cumulative SCV dose of ≥60 Gy versus <60 Gy was 81.3% versus 69.0% (P = 0.042). Compared with Group A or B, Group C showed significantly improved RFS (3y-RFS: 53.8% vs 73.6% vs 100%, p = 0.003) and a numerically longer OS (3y-OS: 73.4% vs 86.7% vs 100%, p = 0.089). Meanwhile, Group C showed the lowest rate of DM as first failure (37.9 % vs 23.5% vs 0 in group A, B and C, respectively, p = 0.010). In patients of Group A, the 3-year OS rates for patients receiving the cumulative SCV dose of ≥60 Gy versus <60 Gy was 78.0% versus 57.3% (p = 0.029).

CONCLUSION

Nodal response to NAT is an independent prognostic factor for survival and pattern of failure. cN3c breast cancer patients with SCLN cCR and ALN pCR after NAT are potentially curable. A cumulative SCV dose of ≥60 Gy is positively associated with improved OS, especially in patients of SCLN without achieving cCR. Our data supports the perspective of optimizing radiotherapeutic strategy based on nodal response.

Genome-Wide Association Study of Body Conformation Traits in a Three-Way Crossbred Commercial Pig Population

Body conformation is the most direct production index, which can fully reflect pig growth status and is closely related to critical economic traits. In this study, we conducted a genome-wide association study (GWAS) on body conformation traits in a population of 1518 Duroc × (Landrace × Yorkshire) commercial pigs. These traits included body length (BL), body height (BH), chest circumference (CC), abdominal circumference (AC), and waist circumference (WC). Both the mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) approaches were employed for the analysis. Our findings revealed 60 significant single nucleotide polymorphisms (SNPs) associated with these body conformation traits in the crossbred pig population. Specifically, sixteen SNPs were significantly associated with BL, three SNPs with BH, thirteen SNPs with CC, twelve SNPs with AC, and sixteen SNPs with WC. Moreover, we identified several promising candidate genes located within the genomic regions associated with body conformation traits. These candidate genes include INTS10, KIRREL3, SOX21, BMP2, MAP4K3, SOD3, FAM160B1, ATL2, SPRED2, SEC16B, and RASAL2. Furthermore, our analysis revealed a novel significant quantitative trait locus (QTL) on SSC7 specifically associated with waist circumference, spanning an 84 kb interval. Overall, the identification of these significant SNPs and potential candidate genes in crossbred commercial pigs enhances our understanding of the genetic basis underlying body conformation traits. Additionally, these findings provide valuable genetic resources for pig breeding programs.

Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs

BACKGROUND

One of the most critical periods for the loss of pig embryos is the 12th day of gestation when implantation begins. Recent studies have shown that non-coding RNAs (ncRNAs) play important regulatory roles during pregnancy. Circular RNAs (circRNAs) are a kind of ubiquitously expressed ncRNAs that can directly regulate the binding proteins or regulate the expression of target genes by adsorbing micro RNAs (miRNA).

RESULTS

We used the Illumina Novaseq6,000 technology to analyze the circRNA expression profile in the endometrium of three Erhualian (EH12) and three Yorkshire (YK12) pigs on day 12 of gestation. Overall, a total of 22,108 circRNAs were identified. Of these, 4051 circRNAs were specific to EH12 and 5889 circRNAs were specific to YK12, indicating a high level of breed specificity. Further analysis showed that there were 641 significant differentially expressed circRNAs (SDEcircRNAs) in EH12 compared with YK12 (FDR < 0.05). Functional enrichment of differential circRNA host genes revealed many pathways and genes associated with reproduction and regulation of embryo development. Network analysis of circRNA-miRNA interactions further supported the idea that circRNAs act as sponges for miRNAs to regulate gene expression. The prediction of differential circRNA binding proteins further explored the potential regulatory pathways of circRNAs. Analysis of SDEcircRNAs suggested a possible reason for the difference in embryo survival between the two breeds at the peri-implantation stage.

CONCLUSIONS

Together, these data suggest that circRNAs are abundantly expressed in the endometrium during the peri-implantation period in pigs and are important regulators of related genes. The results of this study will help to further understand the differences in molecular pathways between the two breeds during the critical implantation period of pregnancy, and will help to provide insight into the molecular mechanisms that contribute to the establishment of pregnancy and embryo loss in pigs.

Genome-Wide Association Study Identifies the Crucial Candidate Genes for Teat Number in Crossbred Commercial Pigs

The number of teats is a crucial reproductive trait with significant economic implications on maternal capacity and litter size. Consequently, improving this trait is essential to facilitate genetic selection for increased litter size. In this study, we performed a genome-wide association study (GWAS) of the number of teats in a three-way crossbred commercial Duroc × (Landrace × Yorkshire) (DLY) pig population comprising 1518 animals genotyped with the 50K BeadChip. Our analysis identified crucial quantitative trait loci (QTL) for the number of teats, containing the ABCD4 and VRTN genes on porcine chromosome 7. Our results establish SNP variants of ABCD4 and VRTN as new molecular markers for improving the number of teats in DLY pigs. Furthermore, the most significant noteworthy single nucleotide polymorphism (SNP) (7_97568284) was identified within the ABCD4 gene, exhibiting a significant association with the total teat number traits. This SNP accounted for a substantial proportion of the genetic variance, explaining 6.64% of the observed variation. These findings reveal a novel gene on SSC7 for the number of teats and provide a deeper understanding of the genetic mechanisms underlying reproductive traits.

Progesterone and Androstenedione Are Important Follicular Fluid Factors Regulating Porcine Oocyte Maturation Quality

Oocytes matured in vitro are useful for assisted human and farm animal reproduction. However, the quality of in vitro matured oocytes is usually lower than that of in vivo matured oocytes, possibly due to the absence of some important signal regulators in vitro. In this study, untargeted metabolomics was used to detect the changes in the metabolites in the follicular fluid (FF) during in vivo pig oocyte maturation and in the culture medium during in vitro maturation. Our results showed that the total metabolite changing profile of the in vivo FF was different from that of the in vitro maturation medium, but the levels of 23 differentially expressed metabolites (DEMs) changed by following the same trend during both in vivo and in vitro pig oocyte maturation. These 23 metabolites may be important regulators of porcine oocyte maturation. We found that progesterone and androstenedione, two factors in the ovarian steroidogenesis pathway enriched from the DEMs, were upregulated in the FF during in vivo pig oocyte maturation. The levels of these two factors were 31 and 20 fold, respectively, and they were higher in the FF than in the culture medium at the oocyte mature stage. The supplementation of progesterone and androstenedione during in vitro maturation significantly improved the pig oocyte maturation rate and subsequent embryo developmental competence. Our finding suggests that a metabolic abnormality during in vitro pig oocyte maturation affects the quality of the matured oocytes. This study identified some important metabolites that regulate oocyte maturation and their developmental potential, which will be helpful to improve assisted animal and human reproduction.

The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs

Genetic mapping to identify genes and alleles associated with or causing economically important quantitative trait variation in livestock animals such as pigs is a major goal in animal genetic improvement. Despite recent advances in high-throughput genotyping technologies, the resolution of genetic mapping in pigs remains poor due in part to the low density of genotyped variant sites. In this study, we overcame this limitation by developing a reference haplotype panel for pigs based on 2259 whole genome-sequenced animals representing 44 pig breeds. We evaluated software combinations and breed composition to optimize the imputation procedure and achieved an average concordance rate in excess of 96%, a non-reference concordance rate of 88%, and an r² of 0.85. We demonstrated in two case studies that genotype imputation using this resource can dramatically improve the resolution of genetic mapping. A public web server has been developed to allow the pig genetics community to fully utilize this resource. We expect this resource to facilitate genetic mapping and accelerate genetic improvement in pigs.

Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs

BACKGROUND

Pork quality can directly affect customer purchase tendency and meat quality traits have become valuable in modern pork production. However, genetic improvement has been slow due to high phenotyping costs. In this study, whole genome sequence (WGS) data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction (GBLUP) for meat quality in large-scale crossbred commercial pigs.

RESULTS

We produced WGS data (18,695,907 SNPs and 2,106,902 INDELs exceed quality control) from 1,469 sequenced Duroc × (Landrace × Yorkshire) pigs and developed a reference panel for meat quality including meat color score, marbling score, L* (lightness), a* (redness), and b* (yellowness) of genomic prediction. The prediction accuracy was defined as the Pearson correlation coefficient between adjusted phenotypes and genomic estimated breeding values in the validation population. Using different marker density panels derived from WGS data, accuracy differed substantially among meat quality traits, varied from 0.08 to 0.47. Results showed that MultiBLUP outperform GBLUP and yielded accuracy increases ranging from 17.39% to 75%. We optimized the marker density and found medium- and high-density marker panels are beneficial for the estimation of heritability for meat quality. Moreover, we conducted genotype imputation from 50K chip to WGS level in the same population and found average concordance rate to exceed 95% and r² = 0.81.

CONCLUSIONS

Overall, estimation of heritability for meat quality traits can benefit from the use of WGS data. This study showed the superiority of using WGS data to genetically improve pork quality in genomic prediction.

A pilot randomized controlled trial evaluating outdoor community walking for knee osteoarthritis: walk

OBJECTIVES

To determine the feasibility of a randomized controlled trial (RCT) examining outdoor walking on knee osteoarthritis (KOA) clinical outcomes and magnetic resonance imaging (MRI) structural changes.

METHOD

This was a 24-week parallel two-arm pilot RCT in Tasmania, Australia. KOA participants were randomized to either a walking plus usual care group or a usual care control group. The walking group trained 3 days/week. The primary outcome was feasibility assessed by changes being required to the study design, recruitment, randomization, program adherence, safety, and retention. Exploratory outcomes were changes in symptoms, physical performance/activity, and MRI measures.

RESULTS

Forty participants (mean age 66 years (SD 1.4) and 60% female) were randomized to walking (n = 24) or usual care (n = 16). Simple randomization resulted in a difference in numbers randomized to the two groups. During the study, class sizes were reduced from 10 to 8 participants to improve supervision, and exclusion criteria were added to facilitate program adherence. In the walking group, total program adherence was 70.0% and retention 70.8% at 24 weeks. The walking group had a higher number of mild adverse events and experienced clinically important improvements in symptoms (e.g., visual analogue scale (VAS) knee pain change in the walking group: - 38.7 mm [95% CI - 47.1 to - 30.3] versus usual care group: 4.3 mm [- 4.9 to 13.4]).

CONCLUSIONS

This study supports the feasibility of a full-scale RCT given acceptable adherence, retention, randomization, and safety, and recruitment challenges have been identified. Large symptomatic benefits support the clinical usefulness of a subsequent trial.

TRIAL REGISTRATION NUMBER

12618001097235. Key Points • This pilot study is the first to investigate the effects of an outdoor walking program on knee osteoarthritis clinical outcomes and MRI joint structure, and it indicates that a full-scale RCT is feasible. • The outdoor walking program (plus usual care) resulted in large improvements in self-reported knee osteoarthritis symptoms compared to usual care alone. • The study identified recruitment challenges, and the manuscript explores these in more details and provides recommendations for future studies.

Identification of candidate genes associated with carcass component weights in commercial crossbred pigs through a combined GWAS approach

In the pork industry chain, carcass cutting is crucial for enhancing the commercial value of pork carcasses. However, the genetic mechanisms underlying carcass component weights remain poorly understood. Here, we used a combined genome-wide association study (GWAS) approach that integrated single- and multi-locus models to map genetic markers and genes associated with the weights of seven carcass components in Duroc × Landrace × Yorkshire (DLY) pigs. As multi-locus GWAS captures more single nucleotide polymorphisms (SNPs) with large effects than single-locus GWAS, the combined GWAS approach detected more SNPs than using the single-locus model alone. We identified 177 nonredundant SNPs associated with these traits in 526 DLY pigs, including boneless butt shoulder (BBS), boneless picnic shoulder (BPS), boneless leg (BL), belly (BELLY), front fat (FF), rear fat (RF) and skin-on whole loin (SLOIN). Using single-locus GWAS, we identified a quantitative trait locus (QTL) for SLOIN on Sus scrofa chromosome 15 (SSC15). Notably, a single SNP (ASGA0069883) in the proximity of this QTL was consistently detected by all GWAS models (one single-locus and four multi-locus models) and explained more than 4% of the phenotypic variance. Our findings suggest that the involved gene, MYO3B, is proposed to be a strong candidate for SLOIN. Further analysis also identified several candidate genes related to BBS (PPP3CA and CPEB4), BPS (ECH1), FF (CACNB2 and ZNF217), BELLY (FGFRL1), BL (CHST11), and RF (LRRK2). The identified SNPs can be used as molecular markers for the genetic improvement of pork carcasses in the molecular-guided breeding of modern commercial pigs.

Uterine luminal-derived extracellular vesicles: potential nanomaterials to improve embryo implantation

Most pregnancy losses worldwide are caused by implantation failure for which there is a lack of effective therapeutics. Extracellular vesicles are considered potential endogenous nanomedicines because of their unique biological functions. However, the limited supply of ULF-EVs prevents their development and application in infertility diseases such as implantation failure. In this study, pigs were used as a human biomedical model, and ULF-EVs were isolated from the uterine luminal. We comprehensively characterized the proteins enriched in ULF-EVs and revealed their biological functions in promoting embryo implantation. By exogenously supplying ULF-EVs, we demonstrated that ULF-EVs improve embryo implantation, suggesting that ULF-EVs are a potential nanomaterial to treat implantation failure. Furthermore, we identified that MEP1B is important in improving embryo implantation by promoting trophoblast cell proliferation and migration. These results indicated that ULF-EVs can be a potential nanomaterial to improve embryo implantation.

Digestion and utilization of plant-based diets by transgenic pigs secreting β-glucanase, xylanase, and phytase in their salivary glands

Novel transgenic (TG) pigs co-expressing three microbial enzymes, β-glucanase, xylanase, and phytase, in their salivary glands were previously generated, which exhibited reduced phosphorus and nitrogen emissions and improved growth performances. In the present study, we attempted to explore the age-related change of the TG enzymic activity, the residual activity of the enzymes in the simulated gastrointestinal tract, and the effect of the transgenes on the digestion of nitrogen and phosphorus content in the fiber-rich, plant-based diets. Results showed that all the three enzymes were stably expressed over the growing and finishing periods in the F2 generation TG pigs. In simulated gastric juice, all the three enzymes exhibited excellent gastrointestinal environment adaptability. The apparent total tract digestibility of phosphorus was increased by 69.05% and 499.64%, while fecal phosphate outputs were decreased by 56.66% and 37.32%, in the TG pigs compared with the wild-type littermates fed with low non-starch polysaccharides diets and high fiber diets, respectively. Over half of available phosphorus and water-soluble phosphorus in fecal phosphorus were reduced. We also found the performance of phosphorus, calcium, and nitrogen retention rates were significantly improved, resulting in faster growth performance in TG pigs. The results indicate that TG pigs can effectively digest the high-fiber diets and exhibit good growth performance compared with wild type pigs.

Genome-wide association study for loin muscle area of commercial crossbred pigs

Objective

Loin muscle area (LMA) is an important target trait of pig breeding. This study aimed to identify single nucleotide polymorphisms (SNPs) and genes associated with LMA in the Duroc × (Landrace × Yorkshire) crossbred pigs (DLY).

Methods

A genome-wide association study (GWAS) was performed using the Illumina 50K chip to map the genetic marker and genes associated with LMA in 511 DLY pigs (255 boars and 256 sows).

Results

After quality control, we detected 35,426 SNPs, including six SNPs significantly associated with LMA in pigs, with MARC0094338 and ASGA0072817 being the two key SNPs responsible for 1.77% and 2.48% of the phenotypic variance of LMA, respectively. Based on previous research, we determined two candidate genes (GHR and OXCT1) that are associated with fat deposition and muscle growth and found further additional genes (MYOCD, ARHGAP44, ELAC2, MAP2K4, FBXO4, FBLL1, RARS1, SLIT3 and RANK3) that are presumed to have an effect on LMA.

Conclusion

This study contributes to the identification of the mutation that underlies quantitative trait loci (QTLs) associated with LMA and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in LMA regulation.

Identification of Important Factors Causing Developmental Arrest in Cloned Pig Embryos by Embryo Biopsy Combined with Microproteomics

The technique of pig cloning holds great promise for the livestock industry, life science, and biomedicine. However, the prenatal death rate of cloned pig embryos is extremely high, resulting in a very low cloning efficiency. This limits the development and application of pig cloning. In this study, we utilized embryo biopsy combined with microproteomics to identify potential factors causing the developmental arrest in cloned pig embryos. We verified the roles of two potential regulators, PDCD6 and PLK1, in cloned pig embryo development. We found that siRNA-mediated knockdown of PDCD6 reduced mRNA and protein expression levels of the pro-apoptotic gene, CASP3, in cloned pig embryos. PDCD6 knockdown also increased the cleavage rate and blastocyst rate of cloned porcine embryos. Overexpression of PLK1 via mRNA microinjection also improved the cleavage rate of cloned pig embryos. This study provided a new strategy to identify key factors responsible for the developmental defects in cloned pig embryos. It also helped establish new methods to improve pig cloning efficiency, specifically by correcting the expression pattern of PDCD6 and PLK1 in cloned pig embryos.

Genome-Wide Association Studies for Flesh Color and Intramuscular Fat in (Duroc × Landrace × Large White) Crossbred Commercial Pigs

The intuitive impression of pork is extremely important in terms of whether consumers are enthusiastic about purchasing it. Flesh color and intramuscular fat (IMF) are indispensable indicators in meat quality assessment. In this study, we determined the flesh color and intramuscular fat at 45 min and 12 h after slaughter (45 mFC, 45 mIMF, 12 hFC, and 12 hIMF) of 1518 commercial Duroc × Landrace × Large White (DLY) pigs. We performed a single nucleotide polymorphism (SNP) genome-wide association study (GWAS) analysis with 28,066 SNPs. This experiment found that the correlation between 45 mFC and 12 hFC was 0.343. The correlation between 45 mIMF and 12 hIMF was 0.238. The heritability of the traits 45 mFC, 12 hFC, 45 mIMF, and 12 hIMF was 0.112, 0.217, 0.139, and 0.178, respectively, and we identified seven SNPs for flesh color and three SNPs for IMF. Finally, several candidate genes regulating these four traits were identified. Three candidate genes related to flesh color were provided: SNCAIP and PRR16 on SSC2, ST3GAL4 on SSC5, and GALR1 on SSC1. A total of three candidate genes related to intramuscular fat were found, including ABLIM3 on SSC2, DPH5 on SSC4, and DOCK10 on SSC15. Furthermore, GO and KEGG analysis revealed that these genes are involved in the regulation of apoptosis and are implicated in functions such as pigmentation and skeletal muscle metabolism. This study applied GWAS to analyze the scoring results of flesh color and IMF in different time periods, and it further revealed the genetic structure of flesh color and IMF traits, which may provide important genetic loci for the subsequent improvement of pig meat quality traits.

Supplementation of SDF1 during Pig Oocyte In Vitro Maturation Improves Subsequent Embryo Development

The quality of in vitro matured oocytes is inferior to that of in vivo matured oocytes, which translates to low developmental capacity of embryos derived from in vitro matured oocytes. The developmental potential of in vitro matured oocytes is usually impaired due to oxidative stress. Stromal cell-derived factor-l (SDF1) can reduce oxidative stress and inhibit apoptosis. The aim of this study was to investigate the effects of SDF1 supplementation during pig oocyte in vitro maturation (IVM) on subsequent embryo development, and to explore the acting mechanisms of SDF1 in pig oocytes. We found that the IVM medium containing 20 ng/mL SDF1 improved the maturation rate of pig oocytes, as well as the cleavage rate and blastocyst rate of embryos generated by somatic cell nuclear transfer, in vitro fertilization, and parthenogenesis. Supplementation of 20 ng/mL SDF1 during IVM decreased the ROS level, increased the mitochondrial membrane potential, and altered the expression of apoptosis-related genes in the pig oocytes. The porcine oocyte transcriptomic data showed that SDF1 addition during IVM altered the expression of genes enriched in the purine metabolism and TNF signaling pathways. SDF1 supplementation during pig oocyte IVM also upregulated the mRNA and protein levels of YY1 and TET1, two critical factors for oocyte development. In conclusion, supplementation of SDF1 during pig oocyte IVM reduces oxidative stress, changes expression of genes involved in regulating apoptosis and oocyte growth, and enhances the ability of in vitro matured pig oocytes to support subsequent embryo development. Our findings provide a theoretical basis and a new method for improving the developmental potential of pig in vitro matured oocytes.

Extracellular vesicle-encapsulated miR-21-5p in seminal plasma prevents sperm capacitation via Vinculin inhibition

To penetrate the zona pellucida before sperm-egg binding, sperm must undergo highly time-controlled capacitation and acrosome reaction in the female reproductive tract. Our previous study demonstrated that miR-21-5p is the most abundant miRNA in boar seminal plasma (SP)-derived extracellular vesicles (EVs) and can target Vinculin (VCL) gene, which may participate in boar sperm capacitation. Thus, this study aims to explore the potential role of miR-21-5p from SP-derived EVs in preventing sperm capacitation and its underlying mechanism. We observed that sperm could incorporate miR-21-5p from SP-derived EVs. The roles of SP-derived EVs miR-21-5p in sperm capacitation were then determined using gain- and loss-of-function analyses. In addition, the expression levels of miR-21-5p, VCL, and VCL protein in liquid-preserved boar sperm following transfection were determined using RT-qPCR and Western blotting. Our results revealed that miR-21-5p overexpression inhibited sperm capacitation and acrosome reaction. Similarly, miR-21-5p expression was significantly lower (P < 0.05) in capacitated sperm than un-capacitated sperm. However, the protein level of VCL was also significantly lower (P < 0.05) in capacitated sperm than un-capacitated sperm. Furthermore, immunofluorescence analysis showed that VCL protein mainly located in sperm head and sperm capacitation was inhibited after treating with VCL protein inhibitor (Chrysin). In conclusion, our study provides reasonable evidence that miR-21-5p expression in SP-derived EVs could prevent sperm capacitation via VCL inhibition.

A Unique Glimpse into the Crosstalk Between Different Epigenetic Mechanisms in Porcine Embryonic Development

The pig is an excellent animal model for simulating human physiology and a major animal for meat production and xenotransplantation. Therefore, researching porcine embryonic development is crucial for studying human reproductive diseases and improving litter size in commercial pigs. Embryonic development in pigs occurs under a complex regulatory mechanism, in which epigenetic regulatory mechanisms play an essential role. Recently, studies on the effects of epigenetic modifications on embryonic development have been conducted at different developmental stages and in different cell lines. Increasing evidence suggests that a certain amount of crosstalk exists between different epigenetic modifications. This review describes four regulatory mechanisms of epigenetics involved in porcine embryonic development: DNA methylation, histone modification, non-coding RNA function, and chromatin accessibility, and explores the possible crosstalk between them.

A composite strategy of genome-wide association study and copy number variation analysis for carcass traits in a Duroc pig population

BACKGROUND

Carcass traits are important in pig breeding programs for improving pork production. Understanding the genetic variants underlies complex phenotypes can help explain trait variation in pigs. In this study, we integrated a weighted single-step genome-wide association study (wssGWAS) and copy number variation (CNV) analyses to map genetic variations and genes associated with loin muscle area (LMA), loin muscle depth (LMD) and lean meat percentage (LMP) in Duroc pigs.

RESULTS

Firstly, we performed a genome-wide analysis for CNV detection using GeneSeek Porcine SNP50 Bead chip data of 3770 pigs. A total of 11,100 CNVs were detected, which were aggregated by overlapping 695 CNV regions (CNVRs). Next, we investigated CNVs of pigs from the same population by whole-genome resequencing. A genome-wide analysis of 21 pigs revealed 23,856 CNVRs that were further divided into three categories (851 gain, 22,279 loss, and 726 mixed), which covered 190.8 Mb (~ 8.42%) of the pig autosomal genome. Further, the identified CNVRs were used to determine an overall validation rate of 68.5% for the CNV detection accuracy of chip data. CNVR association analyses identified one CNVR associated with LMA, one with LMD and eight with LMP after applying stringent Bonferroni correction. The wssGWAS identified eight, six and five regions explaining more than 1% of the additive genetic variance for LMA, LMD and LMP, respectively. The CNVR analyses and wssGWAS identified five common regions, of which three regions were associated with LMA and two with LMP. Four genes (DOK7, ARAP1, ELMO2 and SLC13A3) were highlighted as promising candidates according to their function.

CONCLUSIONS

We determined an overall validation rate for the CNV detection accuracy of low-density chip data and constructed a genomic CNV map for Duroc pigs using resequencing, thereby proving a value genetic variation resource for pig genome research. Furthermore, our study utilized a composite genetic strategy for complex traits in pigs, which will contribute to the study for elucidating the genetic architecture that may be influenced and regulated by multiple forms of variations.

Genetically Engineered Pigs as Efficient Salivary Gland Bioreactors for Production of Therapeutically Valuable Human Nerve Growth Factor

Farm animal salivary glands hold great potential as efficient bioreactors for production of human therapeutic proteins. Nerve growth factor (NGF) is naturally expressed in animal salivary glands and has been approved for human clinical treatment. This study aims to employ transgenic (TG) pig salivary gland as bioreactors for efficient synthesis of human NGF (hNGF). hNGF-TG pigs were generated by cloning in combination with piggyBac transposon-mediated gene transfer. These hNGF-TG pigs specifically expressed hNGF protein in their salivary glands and secreted it at high levels into saliva. Surgical and nonsurgical approaches were developed to efficiently collect saliva from hNGF-TG pigs. hNGF protein was successfully purified from collected saliva and was verified to be biologically active. In an additional step, the double-transgenic pigs, where the endogenous porcine NGF (pNGF) gene was replaced by another copy of hNGF transgene, were created by cloning combined with CRISPR/Cas9-mediated homologous recombination. These double-transgenic pigs expressed hNGF but not pNGF, thus avoiding possible "contamination" of hNGF with pNGF protein during purification. In conclusion, TG pig salivary glands can be used as robust bioreactors for a large-scale synthesis of functional hNGF or other valuable proteins. This new animal pharming method will benefit both human health and biomedicine.

Long non-coding RNA Gm10561 promotes myogenesis by sponging miR-432

Skeletal myogenesis is a highly ordered process finely regulated by various factors. Long non-coding RNAs play an important regulatory role in myogenesis via multiple mechanisms. In this study, we identified the lncRNA Gm10561, which was upregulated during myogenic differentiation and is highly expressed in skeletal muscle. Knockdown of Gm10561 inhibited the proliferation and differentiation of C2C12 myoblasts in vitro and muscle growth in vivo. Overexpression of Gm10561 promoted the proliferation and differentiation of both C2C12 myoblasts and porcine muscle satellite cells. Notably, lncRNA Gm10561 is localized in the cytoplasm and competitively bound to miR-432, which directly targets MEF2C and E2F3. It was confirmed that lncRNA Gm10561 regulates the proliferation and differentiation of myoblasts by acting as a sponge of miR-432 to modulate MEF2C and E2F3 expression. Thus, the lncRNA-Gm10561-miR-432-MEF2C/E2F3 axis plays an important role in myogenesis.

Amphiregulin Supplementation During Pig Oocyte In Vitro Maturation Enhances Subsequent Development of Cloned Embryos by Promoting Cumulus Cell Proliferation

The oocyte in vitro maturation (IVM) technique is important in animal husbandry, biomedicine, and human-assisted reproduction. However, the developmental potential of in vitro matured oocytes is usually lower than that of in vivo matured (IVVM) oocytes. Amphiregulin (AREG) is an EGF-like growth factor that plays critical roles in the maturation and development of mammalian oocytes. This study investigated the effects of AREG supplementation during pig oocyte IVM on the subsequent development of cloned embryos. The addition of AREG to pig oocyte IVM medium improved the developmental competence of treated oocyte-derived cloned embryos by enhancing the expansion and proliferation of cumulus cells (CCs) during IVM. The positive effect of AREG on enhancing the quality of IVVM pig oocytes might be due to the activation of proliferation-related pathways in CCs by acting on the AREG receptor. The present study provides an AREG treatment-based method to improve the developmental competence of cloned pig embryos.

AB0994 Exploring knee osteoarthritis pain trajectories and movement-evoked pain changes during a 24-week outdoor walking program (WALK)

Background

Exercise therapy is recommended as first line treatment for knee osteoarthritis (OA), but it remains to be sub-optimally applied (1). Movement-evoked pain is a potential barrier to exercise adherence, but recent evidence suggests that such pain can be improved by training (2). Walking programs are low-cost, easily adopted and can be performed outdoors which can minimize the risk of SARS-CoV-2 transmission when in a group (3).

Objectives

To explore the acute pain trajectories of individuals with knee OA during a 24-week outdoor walking intervention. In addition, to explore the effect of pain trajectories and/or baseline characteristics on retention and adherence.

Methods

Individuals with clinical knee OA and bone marrow lesions (BMLs) on magnetic resonance imaging (MRI) were asked to follow a 24-week walking program. Every week consisted of two one hour supervised group sessions at various outdoor locations and one unsupervised session. At the start and end of every supervised group walk, knee pain was self-reported by participants to their trainer using a numerical rating scale (NRS) (0-10). The difference between the NRS pain values was considered as an acute pain change evoked by that walk. At baseline, the most affected knee of each participant was assessed using the Visual Analogue Scale (VAS) pain, the Western Ontario and McMasters Universities Osteoarthritis Index (WOMAC) pain, stiffness and function, wellbeing (3 questionnaires) and the Osteoarthritis Research Society International (OARSI) recommended strength and performance measures.

Results

In total, N = 24 participants started the program of whom N = 7 (29%) withdrew. Pain at the start of each walk decreased from NRS 2.5 (SD 1.6) at the first walk (N = 24) to NRS 0.9 (SD 0.8) at the final walk (N = 17). This pain was estimated to decrease on NRS by -0.04 (95% CI -0.05 to -0.02) per supervised session, p < 0.001 during the first 12 weeks and -0.01 (95% CI -0.02 to -0.004), p = 0.004 during the second twelve weeks of the program. The number (%) of participants who experienced an acute increase in pain decreased from 11 (45.8%) at the first walk to 4 (23.5%) at the last walk.

At baseline, non-adherent participants (<70% of group sessions) (N = 11) had lower physical performance scores, including the 30s Chair Stand Test (mean 10 (SD 1.7) stands versus mean 12.0 (SD 1.7) stands, p = 0.011), Fast Past Walk Test (1.23 (SD 0.14) meter per seconds (m/s) vs 1.50 (SD 0.20) m/s, p = 0.001), Six Minute Walk Test (418.8 (SD 75.9) m vs 529 (SD 72.6) m, p = 0.002), compared to adherent participants (N = 13). Non-adherent participants also had less severe self-reported symptoms including WOMAC stiffness (90.7 (SD 44.5) mm vs 121.5 (SD 17.0) mm, p = 0.031), compared to adherent participants. During the first two weeks of walking, acute increases in pain on average (mean ≥0.5 NRS) were reported by a greater number of non-adherent (N = 5 (45.5%)) than adherent participants (n = 4 (30.8%)).

Conclusion

This was an exploratory study and results need to be interpreted with caution due to the small sample size. The walking program resulted in clinically important improvements (MCIIs) (≥ 1 on NRS) (4) in start pain and acute pain changes. Improvements in start pain during the first 12-weeks were comparable to improvements measured in the NEMEX program (2) and may suggest that 12 weeks of exercise is sufficient to achieve MCIIs in pain. Improvements in acute changes in pain were smaller, which may have been related to a floor effect (5). Lower physical performance scores at baseline and more acute increases in pain during the first two weeks was associated with non-adherence. Participants with these characteristics may benefit from a lighter introduction to exercise.

References

[1]Bennell KL, et al. The Lancet Regional Health-Western Pacific. 2021;12:100187.

[2]Sandal LF, et al. Osteoarthritis and cartilage. 2016;24(4):589-92.

[3]Bulfone TC, et al. The Journal of infectious diseases. 2021;223(4):550-61.

[4]Perrot S, et al. Pain. 2013;154(2):248-56.

[5]McHorney CA, et al. Quality of life research. 1995;4(4):293-307.

Acknowledgements

We thank the participants who made this study possible. We would like to acknowledge the research staff, Kate Probert, Lizzy Reid, Simone Fitzgerald, Claire Roberts, Jasmin Ritchie, Dawn Simpson, and Tim Albion. We also thank Hamish Newsham-West for his contribution to the study design.

Disclosure of Interests

Stan Drummen: None declared, Saliu Balogun: None declared, Lieke Scheepers Grant/research support from: Competitive Grant Program Inflammation ASPIRE 2020 Rheumatology International Developed Markets from Pfizer, Employee of: previously worked as an Associate Director Epidemiology at the Medical Evidence Observational Research Department at AstraZeneca., Ishanka Munugoda: None declared, aroub lahham: None declared, Kim Bennell: None declared, Rana Hinman: None declared, Michele Callisaya: None declared, Guoqi Cai: None declared, Petr Otahal: None declared, Tania Winzenberg Consultant of: received payment to create educational material by AMGEN, Zhiqiang Wang: None declared, Benny Antony: None declared, Johanne Martel-Pelletier Shareholder of: ArthroLab Inc., Jean-Pierre Pelletier Shareholder of: ArthroLab Inc., François Abram Consultant of: ArthroLab Inc., Employee of: Arthrolab Inc., Graeme Jones Speakers bureau: received payment for a speakers bureau from Novartis, Dawn Aitken: None declared

Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs

Runs of homozygosity (ROH) are widely used to estimate genomic inbreeding, which is linked to inbreeding depression on phenotypes. However, the adverse effects of specific homozygous regions on phenotypic characteristics are rarely studied in livestock. In this study, the 50 K SNP data of 3,770 S21 Duroc (American origin) and 2,096 S22 Duroc (Canadian origin) pigs were used to investigate the harmful ROH regions on five economic traits. The results showed that the two Duroc lines had different numbers and distributions of unfavorable ROHs, which may be related to the different selection directions and intensities between the two lines. A total of 114 and 58 ROH segments were found with significant adverse effects on the economic traits of S21 and S22 pigs, respectively. Serval pleiotropic ROHs were detected to reduce two or multiple phenotypic performances in two Duroc populations. Candidate genes in these shared regions were mainly related to growth, fertility, immunity, and fat deposition. We also observed that some ROH genotypes may cause opposite effects on different traits. This study not only enhances our understanding of the adverse effects of ROH on phenotypes, but also indicates that ROH information could be incorporated into breeding programs to estimate and control the detrimental effects of homozygous regions.

Urinary metabolomics reveals the biological characteristics of early pregnancy in pigs

Background

Embryo implantation in sows is an important event during pregnancy. During this process, blastocysts undergo dramatic morphologic changes, and the endometrium becomes receptive. Studies have shown that developmental changes associated with the crosstalk between peri-implantation embryos and embryo-uterine are driven by various biomolecules secreted by the endometrium and embryos. In sows, changes in the uterus are also reflected in circulating body fluids and urine. Metabolomics reveals the metabolic state of cells, tissues, and organisms. In this study, we collected urine samples from large white sows during the peri-implantation period. The levels of urinary metabolites at different periods were analyzed using ultra-performance liquid chromatography/tandem mass spectrometry (UPLC–MS/MS) analysis techniques.

Results

A total of 32 samples were collected from 8 sows during the estrus period and at each phase of early pregnancy (9, 12, and 15 days of gestation). A total of 530 metabolites were identified with high confidence in all samples. Compared with samples collected during the estrus phase, 269 differential metabolites were found in samples obtained during early pregnancy.

Conclusions

The identified metabolites included lipids and lipid-like molecules, organic acids and their derivatives, organic oxygen compounds, organoheterocyclic compounds, benzenoids, among others. Metabolites, such as choline and pregnanediol-3-glucuronide, play important roles in pregnancy in sows and other animals. These results reveal the metabolic changes in urine of sows during early pregnancy phase. The differential urinary metabolites can be used for assessing peri-implantation status in sows. Understanding these metabolic changes may promote the management of pregnant sows through various interventions such as provision of proper nutrition.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40813-022-00256-z.

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures of livestock. Commercial breeds provide excellent materials to reveal the landscape of ROH shaped during the intense selection process. Here, we used the GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data of 3,770 American Duroc (AD) and 2,096 Canadian Duroc (CD) pigs to analyze the genome-wide ROH. First, we showed that AD had a moderate genetic differentiation with CD pigs, and AD had more abundant genetic diversity and significantly lower level of inbreeding than CD pigs. In addition, sows had larger levels of homozygosity than boars in AD pigs. These differences may be caused by differences in the selective intensity. Next, ROH hotspots revealed that many candidate genes are putatively under selection for growth, sperm, and muscle development in two lines. Population-specific ROHs inferred that AD pigs may have a special selection for female reproduction, while CD pigs may have a special selection for immunity. Moreover, in the overlapping ROH hotspots of two Duroc populations, we observed a missense mutation (rs81216249) located in the growth and fat deposition-related supergene (ARSB-DMGDH-BHMT) region. The derived allele of this variant originated from European pigs and was nearly fixed in Duroc pigs. Further selective sweep and association analyses indicated that this supergene was subjected to strong selection and probably contributed to the improvement of body weight and length in Duroc pigs. These findings will enhance our understanding of ROH patterns in different Duroc lines and provide promising trait-related genes and a functional-altering marker that can be used for genetic improvement of pigs.