Mapping and functional characterization of structural variation in 1060 pig genomes.

BACKGROUND: Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence. RESULTS: We present a comprehensive SV catalog based on the whole-genome sequence of 1060 pigs (Sus scrofa) representing 101 breeds, covering 9.6% of the pig genome. This catalog includes 42,487 deletions, 37,913 mobile element insertions, 3308 duplications, 1664 inversions, and 45,184 break ends. Estimates of breed ancestry and hybridization using genotyped SVs align well with those from single nucleotide polymorphisms. Geographically stratified deletions are observed, along with known duplications of the KIT gene, responsible for white coat color in European pigs. Additionally, we identify a recent SINE element insertion in MYO5A transcripts of European pigs, potentially influencing alternative splicing patterns and coat color alterations. Furthermore, a Yorkshire-specific copy number gain within ABCG2 is found, impacting chromatin interactions and gene expression across multiple tissues over a stretch of genomic region of ~200 kb. Preliminary investigations into SV's impact on gene expression and traits using the Pig Genotype-Tissue Expression (PigGTEx) data reveal SV associations with regulatory variants and gene-trait pairs. For instance, a 51-bp deletion is linked to the lead eQTL of the lipid metabolism regulating gene FADS3, whose expression in embryo may affect loin muscle area, as revealed by our transcriptome-wide association studies. CONCLUSIONS: This SV catalog serves as a valuable resource for studying diversity, evolutionary history, and functional shaping of the pig genome by processes like domestication, trait-based breeding, and adaptive evolution.

Potential Underestimation of Left Ventricular Mechanical Dyssynchrony in Dyssynchrony and Outcomes Assessment.

Objective: Left ventricular (LV) mechanical dyssynchrony (LVMD) is fundamental to the progression of heart failure and ventricular remodeling. The status of LVMD in different patterns of bundle branch blocks (BBB) is unclear. In this study, we analyzed the relationship between LVMD and left ventricular systolic dysfunction using real-time three-dimensional echocardiography (RT-3DE). Methods: RT-3DE and conventional two-dimensional echocardiography were performed on 68 patients with left bundle branch block (LBBB group), 106 patients with right bundle branch block (RBBB group), and 103 patients without BBB (Normal group). The RT-3DE data sets provided time-volume analysis for global and segmental LV volumes. The LV systolic dyssynchrony index (LVSDI) was calculated using the standard deviation (SD) and maximal difference (Dif) of time to minimum segmental volume (tmsv) for LV segments adjusted by the R-R interval. LVMD was considered if the LVSDI (Tmsv-16-SD) was greater than or equal to 5%. Results: LVSDI is negatively and significantly correlated with left ventricular ejection fraction (LVEF), but not with BBB or QRS duration. The proportion of LVMD in the LBBB, RBBB, and Normal group was 30.88%, 28.30%, and 25.24%, respectively, and there was no significant difference. Conclusion: In dilated cardiomyopathy, LVMD is more closely related to LVEF reduction than QRS morphology and duration.

Clinical features and management of lymphoepithelial cyst.

The aim of the study was to analyze clinical features of lymphoepithelial cyst (LEC) to make a more comprehensive and deeper understanding of it. We retrospectively analyzed the hospital records of 201 patients who were diagnosed by pathology results. Clinical characteristics like demographic profiles, lesion characteristics, therapeutic schedule, and associated costs were analyzed. Patient's age ranged from 17 to 83 years old (52.6 ± 14.3, 120 males and 81 females). There were 12 cases of pancreatic LEC, 48 of oral LEC, and 141 of parotid LEC. Single lesion was found to be more than multiple lesions (147:54, 73.1%:26.9%). The majority of patients was primarily diagnosed by imaging test and endoscopy (171, 85.1%). All patients were finally confirmed by pathology results. Different treatment plans were selected according to personal situation, including dynamic observation (21, 10.5%), non-surgical treatment (24, 11.9%), and surgical treatment (156, 77.6%). No recurrence was found in surgical treatment patients for up to 24 months follow-up. To sum up, LEC is a rare and benign lesion, which is mostly located at parotid and oral, rarely located at pancreas. No typical symptoms could be found. EUS-FNA could be a reliable way to obtain pathological diagnosis. LEC could be cured by surgical resection with no recurrence.

The Incidence and Risk Factors of Acute Myocardial Infarction Among Patients with Gastrointestinal bleeding: A Retrospective Study.

Purpose: Patients with gastrointestinal bleeding (GIB) and acute myocardial infarction (AMI) have higher mortality than that with either GIB or AMI alone. The aims of this study were to determine the incidence and risk factors of AMI in patients with GIB. Patients and Methods: From January 2015 to January 2018, we retrospectively studied 1287 patients with GIB in Renmin Hospital of Wuhan University. Various demographic, laboratory and outcome data were reviewed by charts. Results: Thirty-seven patients had AMI and were placed in AMI group and the rest 1250 patients were in non-AMI group. Patients with AMI were more likely to be older than 70 years, have hypertension, coronary heart disease, chronic kidney disease, and have the recent history of taking aspirin before admission. The ROC curve of hemoglobin (HB) on admission showed area under curve was 0.762, the optimal cut-off value is 76.5g/L. Logistic regression analysis showed that age ≥ 70 years old, coronary heart disease and HB < 76.5g/L on admission were independent risk factors of AMI in patients with GIB. The mortality of patients during hospitalization in AMI group and in non-AMI group were 45.95% and 5.48%, respectively. Patients who displayed a history of liver disease and HB < 76.5g/L on admission had a higher death rate. Conclusion: GIB increased the risk of subsequent AMI, especially in patients over 70 years old, with history of coronary heart disease and HB < 76.5g/L on admission. Patients with GIB and AMI who had history of liver disease and HB < 76.5g/L on admission had a higher mortality rate. Clinicians should identify the high-risk patients of AMI among the GIB population early and prevent AMI.

Differential effects of social isolation on oligodendrocyte development in different brain regions: insights from a canine model.

Social isolation (SI) exerts diverse adverse effects on brain structure and function in humans. To gain an insight into the mechanisms underlying these effects, we conducted a systematic analysis of multiple brain regions from socially isolated and group-housed dogs, whose brain and behavior are similar to humans. Our transcriptomic analysis revealed reduced expression of myelin-related genes specifically in the white matter of prefrontal cortex (PFC) after SI during the juvenile stage. Despite these gene expression changes, myelin fiber organization in PFC remained unchanged. Surprisingly, we observed more mature oligodendrocytes and thicker myelin bundles in the somatosensory parietal cortex in socially isolated dogs, which may be linked to an increased expression of ADORA2A, a gene known to promote oligodendrocyte maturation. Additionally, we found a reduced expression of blood-brain barrier (BBB) structural components Aquaporin-4, Occludin, and Claudin1 in both PFC and parietal cortices, indicating BBB disruption after SI. In agreement with BBB disruption, myelin-related sphingolipids were increased in cerebrospinal fluid in the socially isolated group. These unexpected findings show that SI induces distinct alterations in oligodendrocyte development and shared disruption in BBB integrity in different cortices, demonstrating the value of dogs as a complementary animal model to uncover molecular mechanisms underlying SI-induced brain dysfunction.

iTRAQ-based proteomic analysis of imiquimod in the treatment of ulcerative colitis.

OBJECTIVE: In this study, we explored the potential mechanisms and the signaling pathways involved in the treatment of Ulcerative Colitis (UC) with imiquimod (IMQ). METHODS: The UC mouse model was established by treating C57BL/6J mice with 3% Dextran Sulfate Sodium (DSS). Then, the UC-related symptoms were examined. Disease Activity Index (DAI) was estimated based on weight loss, stool consistency, and occult bleeding or hematochezia. Histological changes were evaluated by Hematoxylin and Eosin (H&E) staining. Furthermore, we used multiplexed Isobaric Tagging for Relative and Absolute Protein Quantification (iTRAQ) technique coupled with high-throughput liquid chromatography tandem mass spectrometry (LC-MS/MS) to determine the differentially expressed proteins (DEPs). RESULTS: Administration of 3% DSS for 7 days induced acute colitis associated with diarrhea, hematochezia, weight loss, and colon shortening. However, after IMQ administration, almost all the above symptoms were improved by different degrees. Specifically, the DAI, histological disorder, and colon shortening were attenuated. In iTRAQ analysis, a total of 4170 proteins were identified with a high confidence (≥ 95% confidence). The numbers of DEPs between the normal and UC model mice, between the normal and the IMQ-treated therapy mice, as well as between the model and the therapy mice were 317, 253, and 209, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the DEPs involved in the complement and coagulation cascades were downregulated in IMQ-treated therapy group. CONCLUSIONS: IMQ might ameliorate colitis by suppressing the complement and coagulation cascades pathway, which might serve as new therapeutic strategies for the treatment of patients with UC.

Effect of mesalazine combined with probiotics on inflammation and immune function of patients with inflammatory bowel disease.

OBJECTIVE: To determine the effects of mesalazine combined with probiotics on inflammation and immune function of patients with inflammatory bowel disease (IBD). METHODS: In this retrospective study, a total of 116 patients with IBD treated in Renmin Hospital of Wuhan University from September 2018 to September 2021 were enrolled and divided into a control group (n=55, treated with mesalazine alone) and a research group (n=61, treated with mesalazine combined with probiotics) according to the treatment regimen. The two groups were compared in the levels of inflammatory factors, immune factors, adverse reactions, clinical efficacy and improvement of patients' disease condition before and after treatment. Logistic regression was used to analyze the independent risk factors of infection in patients with IBD at 6 months after admission. RESULTS: The research group showed a significantly higher the total effective rate than the control group (P<0.05), and there was no notable difference between the two groups in the incidence of adverse reactions (P>0.05). In addition, compared with the control group, the research group showed significantly lower levels of immunoglobulin A (IgA), immunoglobulin G (IgG), immunoglobulin M (IgM), Tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), C-reactive protein (CRP), and had significantly lower scores of clinical activity index (CAI) and endoscopic activity index (EAI) after treatment (all P<0.05). Higher IgG, IgM, IL-6, CRP and EAI levels at admission were independent risk factors for infection in patients with IBD. CONCLUSION: Mesalazine combined with probiotics can substantially improve the disease condition of patients with IBD, improve their immune ability and reduce their inflammation level, with a good safety profile.

Genome-wide identification of functional enhancers and their potential roles in pig breeding.

BACKGROUND: The pig is an economically important livestock species and is a widely applied large animal model in medical research. Enhancers are critical regulatory elements that have fundamental functions in evolution, development and disease. Genome-wide quantification of functional enhancers in the pig is needed. RESULTS: We performed self-transcribing active regulatory region sequencing (STARR-seq) in the porcine kidney epithelial PK15 and testicular ST cell lines, and reliably identified 2576 functional enhancers. Most of these enhancers were located in repetitive sequences and were enriched within silent and lowly expressed genes. Enhancers poorly overlapped with chromatin accessibility regions and were highly enriched in chromatin with the repressive histone modification H3K9me3, which is different from predicted pig enhancers detected using ChIP-seq for H3K27ac or/and H3K4me1 modified histones. This suggests that most pig enhancers identified with STARR-seq are endogenously repressed at the chromatin level and may function during cell type-specific development or at specific developmental stages. Additionally, the PPP3CA gene is associated with the loin muscle area trait and the QKI gene is associated with alkaline phosphatase activity that may be regulated by distal functional enhancers. CONCLUSIONS: In summary, we generated the first functional enhancer map in PK15 and ST cells for the pig genome and highlight its potential roles in pig breeding.

The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks.

Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks. A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses (SC2r-CoVs). Here, we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species, and detected positive signals in muscles of four Manis javanica and, for the first time, one M. pentadactyla. Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia. Using in-solution hybridization capture sequencing, we assembled a partial pangolin SC2r-CoV (pangolin-CoV) genome sequence of 22 895 bp (MP20) from the M. pentadactyla sample. Phylogenetic analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in M. javanica seized by Guangxi Customs. A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated. Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated. Given the potential infectivity of pangolin-CoVs, the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.

IRLnc: a novel functional noncoding RNA contributes to intramuscular fat deposition.

BACKGROUND: Intramuscular fat (IMF) is associated with meat quality and insulin resistance in animals. Research on genetic mechanism of IMF decomposition has positive meaning to pork quality and diseases such as obesity and type 2 diabetes treatment. In this study, an IMF trait segregation population was used to perform RNA sequencing and to analyze the joint or independent effects of genes and long intergenic non-coding RNAs (lincRNAs) on IMF. RESULTS: A total of 26 genes including six lincRNA genes show significantly different expression between high- and low-IMF pigs. Interesting, one lincRNA gene, named IMF related lincRNA (IRLnc) not only has a 292-bp conserved region in 100 vertebrates but also has conserved up and down stream genes (< 10 kb) in pig and humans. Real-time quantitative polymerase chain reaction (RT-qPCR) validation study indicated that nuclear receptor subfamily 4 group A member 3 (NR4A3) which located at the downstream of IRLnc has similar expression pattern with IRLnc. RNAi-mediated loss of function screens identified that IRLnc silencing could inhibit both of the RNA and protein expression of NR4A3. And the in-situ hybridization co-expression experiment indicates that IRLnc may directly binding to NR4A3. As the NR4A3 could regulate the catecholamine catabolism, which could affect insulin sensitivity, we inferred that IRLnc influence IMF decomposition by regulating the expression of NR4A3. CONCLUSIONS: In conclusion, a novel functional noncoding variation named IRLnc has been found contribute to IMF by regulating the expression of NR4A3. These findings suggest novel mechanistic approach for treatment of insulin resistance in human beings and meat quality improvement in animal.

Intelligent difficulty scoring and assistance system for endoscopic extraction of common bile duct stones based on deep learning: multicenter study.

BACKGROUND: The study aimed to construct an intelligent difficulty scoring and assistance system (DSAS) for endoscopic retrograde cholangiopancreatography (ERCP) treatment of common bile duct (CBD) stones. METHODS: 1954 cholangiograms were collected from three hospitals for training and testing the DSAS. The D-LinkNet34 and U-Net were adopted to segment the CBD, stones, and duodenoscope. Based on the segmentation results, the stone size, distal CBD diameter, distal CBD arm, and distal CBD angulation were estimated. The performance of segmentation and estimation was assessed by mean intersection over union (mIoU) and average relative error. A technical difficulty scoring scale, which was used for assessing the technical difficulty of CBD stone removal, was developed and validated. We also analyzed the relationship between scores evaluated by the DSAS and clinical indicators including stone clearance rate and need for endoscopic papillary large-balloon dilation (EPLBD) and lithotripsy. RESULTS: The mIoU values of the stone, CBD, and duodenoscope segmentation were 68.35 %, 86.42 %, and 95.85 %, respectively. The estimation performance of the DSAS was superior to nonexpert endoscopists. In addition, the technical difficulty scoring performance of the DSAS was more consistent with expert endoscopists than two nonexpert endoscopists. A DSAS assessment score ≥ 2 was correlated with lower stone clearance rates and more frequent EPLBD. CONCLUSIONS: An intelligent DSAS based on deep learning was developed. The DSAS could assist endoscopists by automatically scoring the technical difficulty of CBD stone extraction, and guiding the choice of therapeutic approach and appropriate accessories during ERCP.

Gastrointestinal Symptoms Onset in COVID-19 Patients in Wuhan, China.

BACKGROUND: Early detection is critical in limiting the spread of 2019 novel coronavirus (COVID-19). Although previous data revealed characteristics of GI symptoms in COVID-19, for patients with only GI symptoms onset, their diagnostic process and potential transmission risk are still unclear. METHODS: We retrospectively reviewed 205 COVID-19 cases from January 16 to March 30, 2020, in Renmin Hospital of Wuhan University. All patients were confirmed by virus nuclei acid tests. The clinical features and laboratory and chest tomographic (CT) data were recorded and analyzed. RESULTS: A total of 171 patients with classic symptoms (group A) and 34 patients with only GI symptoms (group B) were included. In patients with classical COVID-19 symptoms, GI symptoms occurred more frequently in severe cases compared to non-severe cases (20/43 vs. 91/128, respectively, p < 0.05). In group B, 91.2% (31/34) patients were non-severe, while 73.5% (25/34) patients had obvious infiltrates in their first CT scans. Compared to group A, group B patients had a prolonged time to clinic services (5.0 days vs. 2.6 days, p < 0.01) and a longer time to a positive viral swab normalized to the time of admission (6.9 days vs. 3.3 days, respectively, p < 0.01). Two patients in group B had family clusters of SARS-CoV-2 infection. CONCLUSION: Patients with only GI symptoms of COVID-19 may take a longer time to present to healthcare services and receive a confirmed diagnosis. In areas where infection is rampant, physicians must remain vigilant of patients presenting with acute gastrointestinal symptoms and should do appropriate personal protective equipment.

Genome-wide identification of imprinted genes in pigs and their different imprinting status compared with other mammals.

Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles and plays an essential role in mammalian development and growth. Mammalian genomic imprinting has primarily been studied in mice and humans, with only limited information available for pigs. To systematically characterize this phenomenon and evaluate imprinting status between different species, we investigated imprinted genes on a genome-wide scale in pig brain tissues. Specifically, we performed bioinformatics analysis of high-throughput sequencing results from parental genomes and offspring transcriptomes of hybrid crosses between Duroc and Diannan small-ear pigs. We identified 11 paternally and five maternally expressed imprinted genes in pigs with highly stringent selection criteria. Additionally, we found that the KCNQ1 and IGF2R genes, which are related to development, displayed a different imprinting status in pigs compared with that in mice and humans. This comprehensive research should help improve our knowledge on genomic imprinting in pigs and highlight the potential use of imprinted genes in the pig breeding field.

Effect of fecal microbiota transplantation on experimental colitis in mice.

The aim of the present study was to investigate the effect of fecal microbiota transplantation (FMT) on the acute inflammatory response in a murine model of dextran sulfate sodium (DSS)-induced colitis, and to delineate the putative underlying mechanism(s). Mice were divided into four groups, namely the normal control, DSS, 5-aminosalicylic acid (5-ASA) and FMT group. Mice in the DSS, 5-ASA and FMT groups were orally administered 3% DSS (w/v) solution for 7 days to induce colitis. On days 1, 3, 5 and 7, mice in the DSS, 5-ASA and FMT groups were respectively administered 0.5% carboxymethylcellulose sodium, 5-ASA suspension and fecal suspension by enema. The disease activity index of each mouse was calculated on a daily basis. All mice were sacrificed on day 8, and the length of their colons was measured. Myeloperoxidase (MPO) activity, and the levels of tumor necrosis factor α (TNF-α), interleukin (IL)-1ß and IL-10 in the colon tissues of each group were also measured. Compared with that in the DSS group, FMT ameliorated the severity of inflammation due to ulcerative colitis in mice, which was accompanied by a significantly decreased MPO activity, reduced levels of TNF-α and IL-1ß, and an increased level of IL-10 in colon tissue (all P<0.05). Taken together, these results demonstrated that FMT exerted a therapeutic effect on experimental colitis in mice, and the associated mechanism is likely to involve the remodeling of the intestinal flora and regulation of intestinal T-cell immunity homeostasis.

Genome wide analyses uncover allele-specific RNA editing in human and mouse.

RNA editing is one of the most common RNA level modifications that potentially generate amino acid changes similar to those resulting from genomic nonsynonymous mutations. However, unlike DNA level allele-specific modifications such as DNA methylation, it is currently unknown whether RNA editing displays allele-specificity across tissues and species. Here, we analyzed allele-specific RNA editing in human tissues and from brain tissues of heterozygous mice generated by crosses between divergent mouse strains and found a high proportion of overlap of allele-specific RNA editing sites between different samples. We identified three allele-specific RNA editing sites cause amino acid changes in coding regions of human and mouse genes, whereas their associated SNPs yielded synonymous differences. In vitro cellular experiments confirmed that sequences differing at a synonymous SNP can have differences in a linked allele-specific RNA editing site with nonsynonymous implications. Further, we demonstrate that allele-specific RNA editing is influenced by differences in local RNA secondary structure generated by SNPs. Our study provides new insights towards a better comprehension of the molecular mechanism that link SNPs with human diseases and traits.

Application of 3D visualization and 3D printing technology on ERCP for patients with hilar cholangiocarcinoma.

Endoscopic retrograde cholangiopancreatography (ERCP) is an important treatment for inoperable hilar cholangiocarcinoma (HCC). The aim of the present study as to evaluate the clinical value of three-dimensional visualization (3DV) and 3D printing (3DP) technologies for ERCP in patients with HCC. The clinical data of 15 patients with HCC admitted for ERCP were analyzed retrospectively, including 9 males and 6 females. Thin-sliced data of computed tomography and magnetic resonance cholangiopancreatography (MRCP) were acquired and imported into Mimics Innovation Suite v17.0 software for 3D reconstruction. Standard Template Library files were exported for 3D printing. The target bile duct and Bismuth-Corlette (BC) classification were selected and performed respectively with the aid of Mimics Innovation Suite v17.0 software. The results were compared with the selected ones in ERCP. 3DV and 3DP models were successfully constructed for all patients, which presented the tumor, bile duct and the spatial relationship between them from multiple perspectives. The ERCP of all patients in the present study were performed successfully. The target bile duct screened by them had a high concordance rate of 86.7% with that in ERCP. The diagnostic accuracy of BC type results by 3DV and 3DP models was 93.3%. 3DV and 3DP technologies can accurately show the tumor and its associations with the surrounding bile duct, and it can be used to guide ERCP in HCC patients and improve the success rate of the operation.

PigVar: a database of pig variations and positive selection signatures.

Database URL: http://www.ibiomedical.net/pigvar/.