MALAT1: A Long Non-Coding RNA with Multiple Functions and Its Role in Processes Associated with Fat Deposition.

Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) belongs to the lncRNA molecules, which are involved in transcriptional and epigenetic regulation and the control of gene expression, including the mechanism of chromatin remodeling. MALAT1 was first discovered during carcinogenesis in lung adenocarcinoma, hence its name. In humans, 66 of its isoforms have been identified, and in pigs, only 2 are predicted, for which information is available in Ensembl databases (Ensembl Release 111). MALAT1 is expressed in numerous tissues, including adipose, adrenal gland, heart, kidney, liver, ovary, pancreas, sigmoid colon, small intestine, spleen, and testis. MALAT1, as an lncRNA, shows a wide range of functions. It is involved in the regulation of the cell cycle, where it has pro-proliferative effects and high cellular levels during the G1/S and mitotic (M) phases. Moreover, it is involved in invasion, metastasis, and angiogenesis, and it has a crucial function in alternative splicing during carcinogenesis. In addition, MALAT1 plays a significant role in the processes of fat deposition and adipogenesis. The human adipose tissue stem cells, during differentiation into adipocytes, secrete MALAT1 as one the most abundant lncRNAs in the exosomes. MALAT1 expression in fat tissue is positively correlated with adipogenic FABP4 and LPL. This lncRNA is involved in the regulation of PPARγ at the transcription stage, fatty acid metabolism, and insulin signaling. The wide range of MALAT1 functions makes it an interesting target in studies searching for drugs to prevent obesity development in humans. In turn, in farm animals, it can be a source of selection markers to control the fat tissue content.

Influence of Media Composition on the Level of Bovine Satellite Cell Proliferation.

It is predicted that already in 2040, 35% of requirements for meat will be provided by in vitro production. Recreating the course of myogenesis in vitro, and thus resembling a structure of muscle tissue, is the basis for research focusing on obtaining cultured meat and requires providing relevant factors supporting the proliferation of satellite cells-being precursors of skeletal muscles. The present work aimed to develop the composition of the medium that would most effectively stimulate the proliferation of bovine satellite cells (BSCs). The modeling and optimization methods included the measurements of the synergistic, co-stimulatory effect of three medium components: the amount of glucose, the type of serum (bovine or horse), and the amount of mitogenic factor-bFGF. Additionally, the qPCR analyses determined the expression of genes involved in myogenesis, such as Pax7 and Myogenic Regulatory Factors, depending on the level of the tested factor. The results showed significant positive effects of serum type (bovine serum) and mitogenic factor (addition of 10 ng/mL bFGF) on the proliferation rate. In turn, qPCR analysis displayed no significant differences in the relative expression level of Pax7 genes and MRF factors for both factors. However, a statistically higher Pax7 and Myf5 gene expression level was revealed when a low glucose medium was used (p < 0.05). In conclusion, the components of the medium, such as bovine serum and the addition of a mitogenic factor at the level of 10 ng/mL, ensure a higher proliferation rate of BSCs and lower glucose content ensured the expression of crucial genes in the self-renewal of the satellite cell population.

Equine Metabolic Syndrome: A Complex Disease Influenced by Multifactorial Genetic Factors.

Equine metabolic syndrome (EMS) has become an important issue in modern veterinary medicine and is linked to the common, extremely painful, most-of-the-time performance-terminating hoof laminitis. The growing knowledge in the field of genetic background, inducing environmental factors, diagnosis, treatment and maintenance of affected equines led us to summarise the available information to be used not only for scientific purposes but for fieldwork. In horses, the clinical presentation of EMS includes: obesity or local fat deposition, bilateral lameness or hoof rings attributed to ongoing or previous (pasted) laminitis with the key feature of the occurrence of insulin dysregulation, disturbing the homeostasis within insulin, glucose and lipid metabolism. The management of EMS is based on dietary and fitness discipline; however, intensive research is ongoing in the field of regenerative medicine to develop modern and promising therapies.

Improved antibody pharmacokinetics by disruption of contiguous positive surface potential and charge reduction using alternate human framework.

Optimal pharmacokinetic (PK) properties of therapeutic monoclonal antibodies (mAbs) are essential to achieve the desired pharmacological benefits in patients. To accomplish this, we followed an approach comprising structure-based mAb charge engineering in conjunction with the use of relevant preclinical models to screen and select humanized candidates with PK suitable for clinical development. Murine mAb targeting TDP-43, ACI-5891, was humanized on a framework (VH1-3/VK2-30) selected based on the highest sequence homology. Since the initial humanized mAb (ACI-5891.1) presented a fast clearance in non-human primates (NHPs), reiteration of humanization on a less basic human framework (VH1-69-2/VK2-28) while retaining high sequence homology was performed. The resulting humanized variant, ACI-5891.9, presented a six-fold reduction in clearance in NHPs resulting in a significant increase in half-life. The observed reduced clearance of ACI-5891.9 was attributed not only to the overall reduction in isoelectric point (pI) by 2 units, but importantly to a more even surface potential. These data confirm the importance and contribution of surface charges to mAb disposition in vivo. Consistent low clearance of ACI-5891.9 in Tg32 mice, a human FcRn transgenic mouse model, further confirmed its utility for early assessment and prediction of human PK. These data demonstrate that mAb surface charge is an important parameter for consideration during the selection and screening of humanized candidates in addition to maintaining the other key physiochemical and target binding characteristics.

The Effect of BSCL2 Gene on Fat Deposition Traits in Pigs.

BSCL2 encodes seipin, a transmembrane endoplasmic reticulum protein associated with lipodystrophy and severe metabolic complications, including diabetes and hepatic steatosis. In pigs, BSCL2 expression increases during adipocyte differentiation. In the present study, we identified significant gene variants associated with fat deposition (FD)-related processes based on subcutaneous fat tissue RNA-seq data. In the association study, to prove our hypothesis, three Polish pig breeds were included: Zlotnicka White (ZW, n = 72), Polish Landrace (PL, n = 201), and Polish Large White (PLW, n = 169). Based on variant calling analysis and χ2 tests, BSCL2 mutations showing significantly different genotype/allele distribution between high- and low-fat pigs were selected for a comprehensive association study. Four interesting BSCL2 variants (rs346079334, rs341493267, rs330154033, and rs81333153) belonging to downstream and missense mutations were investigated. Our study showed a significant decrease in minor allele frequency for two BSCL2 variants (rs346079334 and rs341493267) in PL pigs in 2020-2021. In ZW, BSCL2 mutations significantly affected loin and ham fats, meat redness, and growth performance traits, such as feed conversion and daily feed intake. Similar observations were noted for PLW and PL, where BSCL2 mutations influenced fat depositions and meat traits, such as loin eye area, loin mass and fat, carcass yield, and growth performance traits. Based on the observation in pigs, our study supports the theory that BSCL2 expressed in subcutaneous fat is involved in the FD process.

Variations in Fibrinogen-like 1 (FGL1) Gene Locus as a Genetic Marker Related to Fat Deposition Based on Pig Model and Liver RNA-Seq Data.

The goal of this study was to evaluate the effects of mutations in the FGL1 gene associated with pig productive traits to enrich the genetic marker pool for further selection and to support the studies on FGL1 in the context of the fat deposition (FD) process. The variant calling and χ2 analyses of liver RNA-seq data were used to indicate genetic markers. FGL1 mutations were genotyped in the Zlotnicka White (n = 72), Polish Large White (n = 208), Duroc (n = 72), Polish Landrace (PL) (n = 292), and Pulawska (n = 178) pig breeds. An association study was performed using a general linear model (GLM) implemented in SAS® software. More than 50 crucial mutations were identified in the FGL1 gene. The association study showed a significant effect of the FGL1 on intramuscular fat (IMF), loin eye area, backfat thickness at the lumbar, ham mass (p = 0.0374), meat percentage (p = 0.0205), and loin fat (p = 0.0003). Alternate homozygotes and heterozygotes were found in the PL and Duroc, confirming the selective potential for these populations. Our study supports the theory that liver FGL1 is involved in the FD process. Moreover, since fat is the major determinant of flavor development in meat, the FGL1 rs340465447_A allele can be used as a target in pig selection focused on elevated fat levels.

Profiling of genetic markers useful for breeding decision in Selle Francais horse.

Genetic disorders are recognised as hereditary diseases with the most significant economic impact on horse breeding, causing important foal losses, costs of treatments of horses, and maintenance of the mare during the pregnancy. The Selle Francais horses are recognized in many countries and are showing great results in equestrian sports around the world (dressage, show jumping and eventing). The study aimed to detect the presence of three mutant alleles associated with inherited diseases including Fragile Foal Syndrome (FFS), Cerebellar Abiotrophy (CA), Polysaccharide Storage Myopathy (PSSM1) and variant impacting gait type in DMRT3. This trait is important for breeding decision in Selle Francais horses and sheds new light on genetic potential and risks on this breed. The genotyping was performed on 91 Selle Francais horses using PCR-RFLP (for POLD1; GYS1 and DMRT3 genes) and PCR-ACRS (TOE1 gene) methods. The presented report indicated the presence of mutant allele A casual for PSSM1 and allele T associated with FFS syndrome occurrence, in 4% and 6% of analysed horses, respectively. Regarding CA, the present survey did not register any cases of this genetic disorder in Selle Francais horses. Our results show also that about 1% of all the Sell Francais horses studied carry the A allele of DMRT3 gene. The present findings have provided data for these fulness of monitoring genetic diseases and gait type in the investigated breed to avoid losses of offspring.

Investigation of Cerebellar Abiotrophy (CA), Lavender Foal Syndrome (LFS), and Severe Combined Immunodeficiency (SCID) Variants in a Cohort of Three MENA Region Horse Breeds.

Genetic disorders in horses are mostly fatal or usually cause significant economic losses for breeders and owners. Here we studied a total of 177 Arabian, Barb and Arab-Barb horses from the Middle East and North Africa (MENA) using Sanger Sequencing and PCR-ACRS (polymerase chain reaction-artificially created restriction site) approaches to examine the genetic disorders in the studied horse breeds. We identified the genetic variations related to Cerebellar Abiotrophy (CA), Severe Combined Immunodeficiency (SCID) occurrence, and the studied population was free of the mutant allele determined Lavender Foal Syndrome (LFS). Overall, presented data showed that 15 of the studied horses are carriers of two genetic disorders; the investigated horse population showed that five Arabian horses were heterozygous for the CA-associated SNP (rs397160943). The SCID-deletion TCTCA within PRKDC was detected in ten horses (nine Arabian horses and one Arab-Barb horse). This investigation shows the importance of testing these breeds for genetic disorders to avoid further spread of deleterious variants.

Pig Genomics and Genetics.

The pig (Sus scrofa) is the most popular large farm animal in the world [...].

Hypothalamus-pituitary axis transcriptomic modification dependent on growth rate in geese (Anser anser domesticus).

The hypothalamus-pituitary axis is involved in digest processing, stress response, energy storage and many other processes. In birds, this control differs from in mammals, such as regulation of appetite and satiety centre. The transcriptomics analyses of both brain structures can explain and identify the molecular processes related to body growth and development and nutritional status. Many reports describe chicken transcriptome in literature, but gene expression studies in the other poultry species are extremely rare. Therefore, the present research undertook the attempt to explain hypothalamus-pituitary processes in domestic geese-Polish White Koluda®, main Polish line. After 16 weeks of fattening, significant differences in geese weight were observed. Therefore, transcriptome of pituitary and hypothalamus profiles could be compared between low and high growth rate geese groups. Due to the lack of domestic geese genome assembly in the public databases, we used three mapping approaches: de novo analysis, mapping to two other pink-footed and swan geese genomes. The functional examination showed that the most enriched biological process in the geese hypothalamus covered the immune response. Moreover, in the hypothalamus, proteins typical for the pituitary such as PRL and GH were differentially expressed (DE). Our study recommends one gene as a candidate for growth rate in geese-the FOS gene, which encodes Fos proto-oncogene-DE in both analysed tissues. The FOS gene is involved in regulating feeding behaviour, immune regulation, stimulating cellular proliferation and controlling growth hormone synthesis. Moreover, the present investigation indicates DE genes involved in gene expression regulation. The study delivers new information about the changes in the pituitary-hypothalamic axis in geese dependent on growth rate differences.

Transcriptome Analysis for Genes Associated with Small Ruminant Lentiviruses Infection in Goats of Carpathian Breed.

Small ruminant lentiviruses (SRLV) are economically important viral pathogens of sheep and goats. SRLV infection may interfere in the innate and adaptive immunity of the host, and genes associated with resistance or susceptibility to infection with SRLV have not been fully recognized. The presence of animals with relatively high and low proviral load suggests that some host factors are involved in the control of virus replication. To better understand the role of the genes involved in the host response to SRLV infection, RNA sequencing (RNA-seq) method was used to compare whole gene expression profiles in goats carrying both a high (HPL) and low (LPL) proviral load of SRLV and uninfected animals. Data enabled the identification of 1130 significant differentially expressed genes (DEGs) between control and LPL groups: 411 between control and HPL groups and 1434 DEGs between HPL and LPL groups. DEGs detected between the control group and groups with a proviral load were found to be significantly enriched in several gene ontology (GO) terms, including an integral component of membrane, extracellular region, response to growth factor, inflammatory and innate immune response, transmembrane signaling receptor activity, myeloid differentiation primary response gene 88 (MyD88)-dependent toll-like receptor signaling pathway as well as regulation of cytokine secretion. Our results also demonstrated significant deregulation of selected pathways in response to viral infection. The presence of SRLV proviral load in blood resulted in the modification of gene expression belonging to the toll-like receptor signaling pathway, the tumor necrosis factor (TNF) signaling pathway, the cytokine-cytokine receptor interaction, the phagosome, the Ras signaling pathway, the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) (PI3K-Akt) signaling pathway and rheumatoid arthritis. It is worth mentioning that the most predominant in all pathways were genes represented by toll-like receptors, tubulins, growth factors as well as interferon gamma receptors. DEGs detected between LPL and HPL groups were found to have significantly enriched regulation of signaling receptor activity, the response to toxic substances, nicotinamide adenine dinucleotide (NADH) dehydrogenase complex assembly, cytokine production, vesicle, and vacuole organization. In turn, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway tool classified DEGs that enrich molecular processes such as B and T-cell receptor signaling pathways, natural killer cell-mediated cytotoxicity, Fc gamma R-mediated phagocytosis, toll-like receptor signaling pathways, TNF, mammalian target of rapamycin (mTOR) signaling and forkhead box O (Foxo) signaling pathways, etc. Our data indicate that changes in SRLV proviral load induced altered expression of genes related to different biological processes such as immune response, inflammation, cell locomotion, and cytokine production. These findings provide significant insights into defense mechanisms against SRLV infection. Furthermore, these data can be useful to develop strategies against SRLV infection by selection of animals with reduced SRLV proviral concentration that may lead to a reduction in the spread of the virus.

Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland.

This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999.

Single Nucleotide Polymorphisms in Genes Encoding Toll-Like Receptors 7 and 8 and Their Association with Proviral Load of SRLVs in Goats of Polish Carpathian Breed.

Toll-like receptors (TLRs) 7 and 8 are important in single-stranded viral RNA recognition, so genetic variation of these genes may play a role in SRLVs infection and disease progression. Present study aimed to identify SNPs in genes encoding TLR7 and TLR8 in goats of Carpathian breed and analyze their association with the SRLVs provirus concentration as index of disease progression. A total of 14 SNPs were detected, 6 SNPs in the TLR7 gene locus and 8 SNPs in the TLR8 gene. Nine of the 14 identified polymorphisms, 4 in the TLR7 gene and 5 in TLR8 gene, were significantly associated with the SRLVs proviral concentration. These SNPs were located in 3'UTR, 5'UTR and intron sequences as well as in the coding sequences, but they led to silent changes. Homozygous genotypes of three TLR7 SNPs (synonymous variant 1:50703293, 3'UTR variant 1:50701297 and 5'UTR variant 1:50718645) were observed in goats with lower provirus copy number as well as in seronegative animals. The results obtained in this study suggest that SNPs of TLR7/TLR8 genes may induce differential innate immune response towards SRLVs affecting proviral concentration and thereby disease pathogenesis and progression. These findings support a role for genetic variations of TLR7 and TLR8 in SRLVs infection and warrants further studies on the effect of TLR7/TLR8 polymorphisms on SRLVs infection in different populations.

Transcriptome Profiling of the Retained Fetal Membranes-An Insight in the Possible Pathogenesis of the Disease.

Retained fetal membranes (RFM) is one of the most common post-partum diseases of a complex etiology. Moreover, its pathogenesis is still not elucidated. Detailed transcriptomic analysis of physiological and retained placenta may bring profound insight in the pathogenesis of the disease. The aim of the study was to compare the transcriptome of the retained and physiologically released placenta as well as biological pathways and processes in order to determine the possible pathogenesis of the disease. Samples of the endometrium and the allantochorion were taken within 2 h after parturition from control mares (n = 3) and mares with RFM (n = 3). RNA sequencing was performed with the use of all samples and mRNA expression of chosen genes was validated with Real Time PCR. Analysis of RNA-seq identified 487 differentially expressed genes in the allantochorion and 261 in the endometrium of control and RFM mares (p < 0.0001). Within genes that may be important in the release of fetal membranes and were differentially expressed, our report pinpointed BGN, TIMP1, DRB, CD3E, C3, FCN3, CASP3, BCL2L1. Gene ontology analysis showed possible processes which were altered in RFM that are apoptosis, inflammatory-related processes, and extracellular matrix metabolism and might be involved in the pathogenesis of RFM. This is the first report on the transcriptome of RFM and physiologically released placenta in mares.

Distribution of the Warmblood Fragile Foal Syndrome Type 1 Mutation (PLOD1 c.2032G>A) in Different Horse Breeds from Europe and the United States.

Warmblood fragile foal syndrome (WFFS) is an autosomal recessive disorder caused by a single nucleotide variant in the procollagen-lysine-2-oxoglutarate-5-dioxygenase 1 gene (PLOD1:c.2032G>A, p.Gly678Arg). Homozygosity for the PLOD1 variant causes an Ehler-Danlos-like syndrome, which has to date only been reported in warmblood breeds but the WFFS allele has been also detected in the Thoroughbred. To investigate the breed distribution of the WFFS allele, 4081 horses belonging to 38 different breeds were screened. In total, 4.9% of the horses representing 21 breeds carried the WFFS allele. The affected breeds were mainly warmbloods, with carrier frequency as high as 17% in the Hanoverian and Danish Warmblood. The WFFS allele was not detected in most non-warmblood breeds. Exceptions include WFFS carriers in the Thoroughbred (17/716), Haflinger (2/48), American Sport Pony (1/12), and Knabstrupper (3/46). The origin of the WFFS allele remains unknown. The Arabian breed and specifically the stallion Bairactar Or. Ar. (1813), whose offspring were reported to have a similar phenotype in the 19th century, were hypothesized as the origin. DNA from a museum sample of Bairactar Or. Ar. showed that he did not carry the mutated allele. This result, together with the genotypes of 302 Arabians, all homozygous for the reference allele, does not support an Arabian origin of the WFFS allele. Our extensive survey shows the WFFS allele to be of moderate frequency and concern in warmbloods and also in breeds where it may not be expected.

Variability of ACOX1 Gene Polymorphisms across Different Horse Breeds with Regard to Selection Pressure.

The ACOX1 gene encodes peroxisomal acyl-coenzyme A oxidase 1, the first enzyme in the fatty acid ß-oxidation pathway, which could be significant for organisms exposed to long periods of starvation and harsh living conditions. We hypothesized that variations within ACOX1, revealed by RNA Sequencing (RNA-Seq), might be based on adaptation to living conditions and had resulted from selection pressure. There were five different horse breeds used in this study, representing various utility types: Arabian, Thoroughbred, Polish Konik, draft horses, and Hucul. The single-nucleotide polymorphism (SNP) located in the ACOX1 (rs782885985) was used as a marker and was identified using the PCR restriction fragment length polymorphism method (PCR-RFLP). Results indicated extremely different genotype and allele distributions of the ACOX1 gene across breeds. A predominance of the G allele was exhibited in horses that had adapted to difficult environmental conditions, namely, Polish Konik and Huculs, which are considered to be primitive breeds. The prevalence of the T allele in Thoroughbreds indicated that ACOX1 is significant in energy metabolism during flat racing.

Identification of candidate genes and regulatory factors related to growth rate through hypothalamus transcriptome analyses in broiler chickens.

BACKGROUND: Intensive selection for growth rate (GR) in broiler chickens carries negative after-effects, such as aberrations in skeletal development and the immune system, heart failure, and deterioration of meat quality. In Poland, fast-growing chicken populations are highly non-uniform in term of growth rate, which is highly unprofitable for poultry producers. Therefore, the identification of genetic markers for boiler GR that could support the selection process is needed. The hypothalamus is strongly associated with growth regulation by inducing important pituitary hormones. Therefore, the present study used this tissue to pinpoint genes involved in chicken growth control. RESULTS: The experiment included male broilers of Ross 308 strain in two developmental stages, after 3rd and 6th week of age, which were maintained in the same housing and feeding conditions. The obtained results show for the overexpression of genes related to orexigenic molecules, such as neuropeptide Y (NPY), aldehyde dehydrogenase 1 family, member A1 (ALDH1A1), galanin (GAL), and pro-melanin concentrating hormone (PMCH) in low GR cockerels. CONCLUSION: The results reveal strong associations between satiety centre and the growth process. The present study delivers new insights into hypothalamic regulation in broiler chickens and narrows the area for the searching of genetic markers for GR.

Identification of Molecular Mechanisms Related to Pig Fatness at the Transcriptome and miRNAome Levels.

Fat deposition and growth rate are closely related to pork quality and fattening efficiency. The next-generation sequencing (NGS) approach for transcriptome and miRNAome massive parallel sequencing of adipocyte tissue was applied to search for a molecular network related to fat deposition in pigs. Pigs were represented by three breeds (Large White, Pietrain, and Hampshire) that varied in fat content within each breed. The obtained results allowed for the detection of significant enrichment of Gene Ontology (GO) terms and pathways associated directly and indirectly with fat deposition via regulation of fatty acid metabolism, fat cell differentiation, inflammatory response, and extracellular matrix (ECM) organization and disassembly. Moreover, the results showed that adipocyte tissue content strongly affected the expression of leptin and other genes related to a response to excessive feed intake. The findings indicated that modification of genes and miRNAs involved in ECM rearrangements can be essential during fat tissue growth and development in pigs. The identified molecular network within genes and miRNAs that were deregulated depending on the subcutaneous fat level are proposed as candidate factors determining adipogenesis, fatness, and selected fattening characteristics in pigs.

Use of the HRM Method in Quick Identification of FecXO Mutation in Highly Prolific Olkuska Sheep.

Olkuska is a highly prolific sheep breed in Poland. Thanks to earlier identification of the genetic basis of its prolificacy, a mutation in the BMP-15 gene, we can use molecular biology tools to identify this causative mutation affecting prolificacy. In our research, we used the High-Resolution Melting (HRM) and Sanger sequencing methods to identify the genotypes of the studied animals. The result obtained by the HRM method is identical to those obtained by the sequencing method, which confirms the effectiveness of the HRM method and the possibility of quick and cheap identification of individuals with a FecXO mutation.