Weighted gene co-expression network analysis identifies important modules and hub genes involved in the regulation of breast muscle yield in broilers.

Objective: Increasing breast meat production is one of the primary goals of the broiler industry. Over the past few decades, tremendous progress has been made in genetic selection and the identification of candidate genes for improving the breast muscle mass. However, the molecular network contributing to muscle production traits in chickens still needs to be further illuminated. Methods: A total of 150 1-day-old male 817 broilers were reared in a floor litter system. At the market age of 50 d, eighteen healthy 817 broilers were slaughtered and the left pectoralis major muscle sample from each bird was collected for RNA-seq sequencing. The birds were then plucked and eviscerated and the whole breast muscle was removed and weighed. Breast muscle yield was calculated as the ratio of the breast muscle weight to the eviscerated weight. To identify the co-expression networks and hub genes contributing to breast muscle yield in chickens, we performed weighted gene co-expression network analysis (WGCNA) based on the 18 transcriptome datasets of pectoralis major muscle from eighteen 817 broilers. Results: The WGCNA analysis classified all co-expressed genes in the pectoral muscle of 817 broilers into 44 modules. Among these modules, the turquoise and skyblue3 modules were found to be most significantly positively (r=0.78, p=1e-04) and negatively (r=-0.57, p=0.01) associated with breast meat yield, respectively. Further analysis identified several hub genes (e.g., DLX3, SH3RF2, TPM1, CAV3, MYF6, and CFL2) that involved in muscle structure and muscle development were identified as potential regulators of breast meat production. Conclusion: The present study has advanced our understanding of the molecular regulatory networks contributing to muscle growth and breast muscle production and will contribute to the molecular breeding of chickens in the future.

To explore the pathogenesis of anterior resection syndrome by magnetic resonance imaging rectal defecography.

BACKGROUND: Over 90% of rectal cancer patients develop low anterior resection syndrome (LARS) after sphincter-preserving resection. The current globally recognized evaluation method has many drawbacks and its subjectivity is too strong, which hinders the research and treatment of LARS. AIM: To evaluate the anorectal function after colorectal cancer surgery by quantifying the index of magnetic resonance imaging (MRI) defecography, and pathogenesis of LARS. METHODS: We evaluated 34 patients using the standard LARS score, and a new LARS evaluation index was established using the dynamic images of MRI defecography to verify the LARS score. RESULTS: In the LARS score model, there were 10 (29.41%) mild and 24 (70.58%) severe cases of LARS. The comparison of defecation rate between the two groups was 29.36 ± 14.17% versus 46.83 ± 18.62% (P = 0.004); and MRI-rectal compliance (MRI-RC) score was 3.63 ± 1.96 versus 7.0 ± 3.21 (P = 0.001). Severe and mild LARS had significant differences using the two evaluation methods. There was a significant negative correlation between LARS and MRI-RC score (P < 0.001), and they had a negative correlation with defecation rate (P = 0.028). CONCLUSION: MRI defecography and standard LARS score can both be used as an evaluation index to study the pathogenesis of LARS.

Identification of Key Modules and Hub Genes Involved in Regulating the Color of Chicken Breast Meat Using WGCNA.

Meat color is one of the most important economic traits in chickens. However, the gene network and regulatory mechanisms contributing to meat color traits in chickens remain largely unknown. In the present study, we performed weighted gene co-expression network analysis (WGCNA) based on RNA-Seq datasets of 16 pectoralis major muscle samples from two yellow-feather chicken breeds to identify the modules and hub genes related to meat color in chickens. A total of 18,821 genes were used to construct the weighted gene co-expression network, and 29 co-expression gene modules were identified. Among these modules, five modules including blue, brown, steel blue, paleturquoise and orange modules were found to be significantly correlated with meat color traits. Furthermore, several genes within the association module involved in the regulation of mitochondrial activity (e.g., ATP5L, UQCR10 and COX7C) and lipid oxidation (e.g., CAV3, RBP4A and APOH) were identified as hub genes that may play a crucial role in the regulation of meat color. These results provide valuable information to improve our understanding of gene expression and regulation in relation to meat color traits and contribute to future molecular breeding for improving meat color in chickens.

Genome-wide scan for selection signatures and genes related to heat tolerance in domestic chickens in the tropical and temperate regions in Asia.

Heat stress is one of the major environmental stressors challenging the global poultry industry. Identifying the genes responsible for heat tolerance is fundamentally important for direct breeding programs. To uncover the genetic basis underlying the ambient temperature adaptation of chickens, we analyzed a total of 59 whole genomes from indigenous chickens that inhabit South Asian tropical regions and temperate regions from Northern China. We applied FST and π-ratio to scan selective sweeps and identified 34 genes with a signature of positive selection in chickens from tropical regions. Several of these genes are functionally implicated in metabolism (FABP2, RAMP3, SUGCT, and TSHR) and vascular smooth muscle contractility (CAMK2), and they may be associated with adaptation to tropical regions. In particular, we found a missense mutation in thyroid-stimulating hormone receptor (41020238:G>A) that shows significant differences in allele frequency between the chicken populations of the two regions. To evaluate whether the missense mutation in TSHR could enhance the heat tolerance of chickens, we constructed segregated chicken populations and conducted heat stress experiments using homozygous mutations (AA) and wild-type (GG) chickens. We found that GG chickens exhibited significantly higher concentrations of alanine aminotransferase, lactate dehydrogenase, and creatine kinase than AA chickens under heat stress (35 ± 1°C) conditions (P < 0.05). These results suggest that TSHR (41020238:G>A) can facilitate heat tolerance and adaptation to higher ambient temperature conditions in tropical climates. Overall, our results provide potential candidate genes for molecular breeding of heat-tolerant chickens.

MicroRNA-766-3p-mediated downregulation of HNF4G inhibits proliferation in colorectal cancer cells through the PI3K/AKT pathway.

Nuclear receptors (NRs) are a class of transcription factors that play a pivotal role in carcinogenesis, but their function in colorectal cancer (CRC) remains unclear. Here, we investigate the role NRs play in CRC pathogenesis. We found that hepatocyte nuclear factor 4 gamma (HNF4G; NR2A2), hepatocyte nuclear factor 4α (HNF4A; NR2A1), and retinoid-related orphan receptor γ (RORC; NR1F3) were significantly upregulated in CRC tissues analyzed by GEPIA bioinformatics tool. The expression of HNF4G was examined in CRC samples and cell lines by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry. Increased expression of HNF4G was strongly associated with high tumor-node-metastasis stage and poor prognosis. Moreover, overexpression of HNF4G significantly promoted the proliferation of CRC cells in vitro. Next, we found that HNF4G promoted CRC proliferation via the PI3K/AKT pathway through targeting of GNG12 and PTK2. In addition, HNF4G was verified as a direct target of microRNA-766-3p (miR-766-3p). miR-766-3p inhibited the proliferation of CRC cells by targeting HNF4G in vitro and in vivo. Collectively, our study indicates that miR-766-3p reduces the proliferation of CRC cells by targeting HNF4G expression and thus inhibits the PI3K/AKT pathway. Therefore, development of therapies which target the miR-766-3p/HNF4G axis may aid in the treatment of CRC.

Multiple organ dysfunction due to a rare complication of Nuss procedure for pectus excavatum: A case report.

A 19-year-old male patient who suffered from sudden and repeated multiple organ dysfunction syndrome one month after the bar removal procedure of Nuss surgery for pectus excavatum was admitted to our department. With organ function supportive treatment, the etiology was finally identified to be a bone spur located at the inner border of the left costa due to repeated friction between the implanted steel bar and the rib, which damaged the heart repeatedly and induced the consequent acute cardiac tamponade. After operation, the patient was successfully managed and discharged. Follow-ups till three years indicated a good recovery.

Per-, poly-fluoroalkyl substances (PFASs) pollution in benthic riverine ecosystem: Integrating microbial community coalescence and biogeochemistry with sediment distribution.

Per-, Poly-fluoroalkyl substances (PFASs) accumulation in benthic environments is mainly determined by material mixing and represents a significant challenge to river remediation. However, less attention has been paid to the effects of sediment distribution on PFASs accumulation, and how PFASs influence microbial community coalescence and biogeochemical processes. In order to identify correlations between PFASs distribution and benthic microbial community functions, we conducted a field study and quantified the ecological constrains of material transportation on benthic microorganisms. Perfluorohexanoic acid (PFHxA) contributed most to the taxonomic heterogeneity of both archaeal (12.199%) and bacterial (13.675%) communities. Genera Methanoregula (R2 = 0.292) and Bacillus (R2 = 0.791) were identified as indicators that respond to PFASs. Phylogenetic null modeling indicated that deterministic processes (50.0-82.2%) dominated in spatial assembly of archaea, while stochasticity (94.4-97.8%) dominated in bacteria. Furthermore, spatial mixing of PFASs influenced broadly in nitrogen cycling of archaeal genomes, and phosphorus mineralization of bacterial genomes (p < 0.05). Overall, we quantified the effect of PFASs on community assembly and highlighted the constrains of PFASs influence on benthic geochemical potentials, which may provide new insights into riverine remediation.

Exercise profile and effect on growth traits, carcass yield, meat quality, and tibial strength in Chinese Wannan chickens.

The aim of the study was to understand the dynamic changes in daily step counts (DSC) during the development of chickens and to further explore the effects of exercise on the growth performance, carcass yield, meat quality, and tibial strength of cocks. A total of 600 (half male and half female) 1-day-old Wannan chickens with similar hatching weights were raised under the same rearing conditions. All birds were wing banded and housed in identical cages for from 1 to 8 wk in the experimental poultry house. The dimensions of the cages were 70 × 70 × 40 cm (length × width × height). At the age of 9 to 16 wk, these birds were reared in indoor pens (2 m × 2 m, 1,000 cm2 per bird). In addition, they also had a free-range grass paddock (20 m × 30 m, 1 m2 per bird). The DSC of male and female Wannan chicks were recorded from 70 to 112 d by using a pedometer. At 112 d of age, based on the average DSC, birds were divided into groups representing the highest (HS), medium, and lowest (LS) number of step groups. Fifteen cocks from each group were selected for subsequent experiments. Compared with the LS group, the HS group displayed higher tibial strength (P = 0.025) and lower BW, cooking loss (P = 0.014), shear force (P = 0.023), and drip loss (P = 0.008). The DSC had no effects on the female BW or male carcass parameters. There was no significant change in the DSC of all birds from 70 to 112 d. However, male chickens took more steps than females at 15 (P = 0.025) and 16 (P = 0.012) week of age. In conclusion, the effects of the DSC on the BW of Wannan chickens depend on sex, and enhanced exercise could improve the meat quality and tibial strength of cocks.

Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses.

Although domestic ducks have been important poultry species throughout human history, their origin remains enigmatic, with mallards and/or Chinese spot-billed ducks being proposed as the direct wild ancestor(s) of domestic ducks. Here, we analyzed 118 whole genomes from mallard, Chinese spot-billed, and domestic ducks to reconstruct their evolutionary history. We found pervasive introgression patterns among these duck populations. Furthermore, we showed that domestic ducks separated from mallard and Chinese spot-billed ducks nearly 38 thousand years ago (kya) and 54 kya, respectively, which is considerably outside the time period of presumed duck domestication. Thus, our results suggest that domestic ducks may have originated from another wild duck population that is currently undefined or unsampled, rather than from present-day mallard and/or Chinese spot-billed ducks, as previously thought. Overall, this study provides new insight into the complex evolution of ducks.

Amlexanox attenuates experimental autoimmune encephalomyelitis by inhibiting dendritic cell maturation and reprogramming effector and regulatory T cell responses.

BACKGROUND: Amlexanox (ALX), a TBK1 inhibitor, can modulate immune responses and has anti-inflammatory properties. To investigate its role in regulating the progression of experimental autoimmune encephalomyelitis (EAE), we studied the effect of ALX on the maturation of dendritic cells (DCs) and the responses of effector and regulatory T cells (Tregs). METHODS: In vitro, bone marrow-derived DCs (BMDCs) were cultured and treated with ALX. Their proliferation, maturation, and their stimulatory function to induce T cells responses were detected. In vivo, the development of EAE from different groups was recorded. At the peak stage of disease, HE, LFB, and electronic microscope (EM) were used to evaluate inflammation and demyelination. Maturation of splenic DC and Th1/Th17/Treg response in the CNS and peripheral were also detected. To further explore the mechanism underlying the action of ALX in DC maturation, the activation of TBK1, IRF3, and AKT was analyzed. RESULTS: Our data indicated that ALX significantly inhibited the proliferation and maturation of BMDCs, characterized by the reduced MHCII, a co-stimulatory molecule, IL12, and IL-23 expression, along with morphological alterations. Co-culture of ALX-treated BMDCs inhibited allogeneic T cell proliferation and MOG-specific T cell response. In EAE mice, ALX significantly attenuated the EAE development by decreasing inflammatory infiltration and demyelination in the spinal cords, accompanied by reduced frequency of splenic pathogenic Th1 and Th17 cells and increased Tregs. Moreover, ALX treatment decreased Th1 and Th17 cytokines, but increased Treg cytokines in the CNS and spleen. Notably, ALX treatment reduced the frequency and expression of CD80 and CD86 on splenic DCs and lowered IL-12 and IL-23 secretion, further supporting an impaired maturation of splenic DCs. In addition, ALX potently reduced the phosphorylation of IRF3 and AKT in BMDC and splenic DCs, both of which are substrates of TBK1 and associated with DC maturation. CONCLUSIONS: ALX, a TBK1 inhibitor, mitigated EAE development by inhibiting DC maturation and subsequent pathogenic Th1 and Th17 responses while increasing Treg responses through attenuating the TBK1/AKT and TBK1/IRF3 signaling.

Perianal Infections in the Phase before Engraftment after Allogeneic Hematopoietic Stem Cell Transplantations: A Study of the Incidence, Risk Factors, and Clinical Outcomes.

In this study, we aimed to investigate the incidence, risk factors, and clinical outcomes of perianal infections during the pre-engraftment phase after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Consecutive patients who underwent non-T-cell-depleted allo-HSCT at the Peking University Institute of Hematology from January 1 to December 31, 2016 were enrolled (n = 646). Ninety-nine patients were found to have perianal infections during the pre-engraftment phase, and 80 were found to have neutropenia on perianal infection diagnosis. The cumulative incidence of perianal infection during the pre-engraftment phase after allo-HSCT was 15.3%. A history of perianal infection (hazard ratio [HR] = 15.28, p < 0.001) or hemorrhoids before allo-HSCT (HR = 3.09, p = 0.001) was significantly associated with the new occurrence of perianal infection after allo-HSCT. All patients received empirical broad-spectrum antimicrobial therapies, and 97 were cured after treatment. The clinical outcomes at 100 days after allo-HSCT were comparable in patients with and without perianal infections. In summary, patients who had perianal infection or hemorrhoids before allo-HSCT had a higher risk of new occurrence of perianal infection after allo-HSCT. With appropriate treatment, perianal infection during the pre-engraftment phase did not influence the clinical outcomes.

Wall Imaging for Unilateral Intracranial Vertebral Artery Hypoplasia with Three-dimensional High-isotropic Resolution Magnetic Resonance Images.

BACKGROUND: There are few studies for evaluating wall characteristics of intracranial vertebral artery hypoplasia (VAH). The aim of this study was to determine wall characteristics of VAH with three-dimensional volumetric isotropic turbo spin echo acquisition (3D VISTA) images and differentiate between acquired atherosclerotic stenosis and VAH. METHODS: Thirty patients with suspicious VAH by luminograms were retrospectively enrolled between January 2014 and February 2015. The patients were classified as "acquired atherosclerotic stenosis" or "VAH" based on 3D VISTA images. The wall characteristics of VAH were assessed to determine the presence of atherosclerotic lesions, and the patients were classified into two subgroups (VAH with atherosclerosis and VAH with normal wall). Wall characteristics of basilar arteries and vertebral arteries were also assessed. The clinical and wall characteristics were compared between the two groups. RESULTS: Five of 30 patients with suspicious VAH were finally diagnosed as acquired atherosclerotic stenosis by 3D VISTA images. 25 patients were finally diagnosed as VAH including 16 (64.00%) patients with atherosclerosis and 9 (36.00%) patients with normal wall. In the 16 patients with atherosclerosis, plaque was found in 9 patients, slight wall thickening in 6 patients, and thrombus and wall thickening in 1 patient. Compared with VAH patients with normal wall, VAH patients with atherosclerosis showed atherosclerotic basilar arteries and dominant vertebral arteries more frequently (P = 0.000). CONCLUSIONS: Three-dimensional VISTA images enable differentiation between the acquired atherosclerotic stenosis and VAH. VAH was also prone to atherosclerotic processes.

Expressions of connexin 32 and 26 and their correlation to prognosis of non-small cell lung cancer.

BACKGROUND AND OBJECTIVE: Gap junction intercellular communication (GJIC) plays an important role in regulating homeostasis and differentiation in many tissues. Connexins are gap junction proteins, whose expressions directly affect the function of GJIC. This study was to investigate expressions of connexin 32 and 26 proteins in non-small cell lung cancer (NSCLC), and their correlation to clinicopathological characters of NSCLC. METHODS: Immunohistochemistry was applied to detect expressions of connexin 32 and 26 in 77 NSCLC tissues. Correlations of connexin 32 and 26 expressions to smoking, tumor size, histological type, the degree of differentiation, lymph node metastasis and prognosis were analyzed. RESULTS: The positive rates of connexin 32 and 26 were 51.9% and 40.3% in the 77 samples, which were significantly higher than 20.3% and 30.5% in alveolar epithelium (p = 0.000, r = -0.322; p = 0.013, r = -0.215). Positive expression of connexion 32 was positively correlated with the differentiation degree of NSCLC tissues (p = 0.010, r = 0.345). The one- to five-year survival rates were higher in patients with positive connexion 32 expression than those without (p = 0.005). Moreover, the positive rate of connexin 26 was not correlated to smoking, tumor size, histological type, the degree of differentiation, lymph node metastasis and the postoperative survival time (p > 0.05). CONCLUSIONS: Expression of connexin 32 is closely correlated to the differentiation of NSCLC and affects the prognosis of NSCLC patients. Increasing the expression of connexin 32 may improve the prognosis of NSCLC.

[Expression and significance of CD44(+)ESA(+)CD24(-/low), stem cell markers for breast cancer, in non-small-cell lung carcinoma].

BACKGROUND & OBJECTIVE: Stem cells are found in all human tissues, while tumor stem cells (TSCs) are also detected in tumors. TSC of breast cancer has been separated and its markers have been affirmed. However, TSC of lung carcinoma has not been separated yet. This study was to investigate the expression and significance of stem cell markers for breast cancer (CD44(+)ESA(+)CD24(-/low)) in non-small-cell lung carcinoma (NSCLC). METHODS: Expressions of CD44,ESA and CD24 of tumor tissues in 77 cases of NSCLC patients were detected using immunohistochemistry. The correlations of the expression of the makers to tumor size, smoking, histological type, differentiation, lymphoid metastasis, and prognosis were analyzed. RESULTS: The expressive rates of CD44,ESA and CD24 were 63.6%, 66.2% and 7.8%, respectively in 77 NSCLC tissues. CD44-positive expression was significantly higher in poorly differentiated and undifferentiated group than in well differentiated group. ESA-positive expression was significantly higher in well differentiated group than in poorly differentiated and undifferentiated group. The ESA positivity was significantly higher in glandular carcinoma than in squamous carcinoma. The expressive rate of CD44(+)ESA(+)CD24(-/low) in 77 cases of NSCLC was 36.4%. No correlations were found in the expression of CD44(+)ESA(+)CD24(-/low) to smoking, tumor size, histological type, differentiation, lymphoid metastasis and prognosis (P>0.05). CONCLUSION: Expressions of stem cell markers for breast cancer (CD44(+)ESA(+)CD24(-/low)) are not associated with tumor size, histological type, differentiation, lymphoid metastasis and prognosis of NSCLC.