Large-scale profiling and identification of potential regulatory mechanisms for allelic gene expression in colorectal cancer cells

Allelic variation in gene expression is common in humans and this variation is associated with phenotypic variation. In this study, we employed high-density single nucleotide polymorphism (SNP) chips containing 13,900 exonic SNPs to identify genes with allelic gene expression in cells from colorectal cancer cell lines. We found 2 monoallelically expressed genes (ERAP2 and MYLK4), 32 genes with an allelic imbalance in their expression, and 13 genes showing allele substitution by RNA editing. Among a total of 34 allelically expressed genes in colorectal cancer cells, 15 genes (44.1%) were associated with cis-acting eQTL, indicating that large portions of allelically expressed genes are regulated by cis-acting mechanisms of gene expression. In addition, potential regulatory variants present in the proximal promoter regions of genes showing either monoallelic expression or allelic imbalance were not tightly linked with coding SNPs, which were detected with allelic gene expression. These results suggest that multiple rare variants could be involved in the cis-acting regulatory mechanism of allelic gene expression. In the comparison with allelic gene expression data from Centre d'Etude du Polymorphisme Humain (CEPH) family B cells, 12 genes showed B-cell specific allelic imbalance and 1 noncoding SNP showed colorectal cancer cell-specific allelic imbalance. In addition, different patterns of allele substitution were observed between B cells and colorectal cancer cells. Overall, our study not only indicates that allelic gene expression is common in colorectal cancer cells, but our study also provides a better understanding of allele-specific gene expression in colorectal cancer cells.     

ATP binding cassette G1-dependent cholesterol efflux during inflammation

ATP binding cassette transporter G1 (ABCG1) mediates the transport of cellular cholesterol to HDL, and it plays a key role in maintaining macrophage cholesterol homeostasis. During inflammation, HDL undergoes substantial remodeling, acquiring lipid changes and serum amyloid A (SAA) as a major apolipoprotein. In the current study, we investigated whether remodeling of HDL that occurs during acute inflammation impacts ABCG1-dependent efflux. Our data indicate that lipid free SAA acts similarly to apolipoprotein A-I (apoA-I) in mediating sequential efflux from ABCA1 and ABCG1. Compared with normal mouse HDL, acute phase (AP) mouse HDL containing SAA exhibited a modest but significant 17% increase in ABCG1-dependent efflux. Interestingly, AP HDL isolated from mice lacking SAA (SAAKO mice) was even more effective in promoting ABCG1 efflux. Hydrolysis with Group IIA secretory phospholipase A(2) (sPLA(2)-IIA) significantly reduced the ability of AP HDL from SAAKO mice to serve as a substrate for ABCG1-mediated cholesterol transfer, indicating that phospholipid (PL) enrichment, and not the presence of SAA, is responsible for alterations in efflux. AP human HDL, which is not PL-enriched, was somewhat less effective in mediating ABCG1-dependent efflux compared with normal human HDL. Our data indicate that inflammatory remodeling of HDL impacts ABCG1-dependent efflux independent of SAA.     

Synchronization of ovulation and fertility in weaned sows treated with intravaginal triptorelin is influenced by timing of administration and follicle size

A 100 μg dose of triptorelin was tested for synchronizing ovulation in sows. In Experiment 1, conducted in April through June, sows (n = 125) were assigned to Control (untreated), TG-96 (Triptorelin Gel (TG) given intravaginally at 96 h post-weaning), or TG-E (given intravaginally at estrus). To optimize AI timing, sows were inseminated at 2 and 26 h after estrus for Control and TG-E and at 8 and 32 h following TG-96. Ovulation by 48 h post-treatment tended to be affected by treatment (P = 0.08) and more (P < 0.05) TG-96 sows ovulated (57.9%) compared to Controls (34.2%), but TG-E (45.1%) did not differ (P > 0.10). Duration of estrus was reduced (P < 0.005) in TG-96 (51 h) and TG-E (58 h) compared to Controls (65 h). There was no treatment effect on farrowing rate (71%) or total born (10.4). Average follicle size <6.5 mm at 96 h after weaning was associated with reduced (P < 0.01) estrus, ovulation and farrowing rate. Experiment 2 was conducted in August through September using 503 weaned sows. The TG-96 treatment reduced duration of estrus (P = 0.03), but treatment did not affect estrus expression, farrowing rate or total pigs born. In conclusion, use of a 100 μg dose of triptorelin intravaginally at 96 h or at estrus advanced ovulation and when used with timed insemination, resulted in similar farrowing rates and litter sizes comparable to sows mated based on estrus. However, ovulation induction and timed AI success may benefit from an approach that ensures sows have adequate follicle development at time of treatment.     

Pregnancy rates following AI with sexed semen in Mediterranean Italian buffalo heifers (Bubalus bubalis)

The use of sexed semen in farm animal production and genetic improvement has been shown to be feasible with variable degree of efficiency in a number of species, and proved to be economically viable in cattle. In the last two decades, various newly developed reproductive technologies applicable in buffaloes have mushroomed. Recently, following the birth of the first buffalo calves using AI with sexed semen, commercial interest to exploit sexing of semen in this species too is aroused. In order to verify the successful adoption of this technology in the buffalo, the present study on the use of sexed semen for AI was carried out and compared with conventional artificial insemination using nonsexed semen. A total of 379 buffalo heifers were used for synchronization of ovulation using the Presynch protocol in the South of Italy. Selected animals at the time of AI were randomly allocated to three different experiment groups: (1) 102 animals subjected to AI in the body of the uterus with sexed semen (SS body); (2) 104 animals subjected to AI in the horn of the uterus with sexed semen (SS horn); and (3) 106 animals subjected to AI in the body of the uterus with conventional nonsexed semen (NSS body). Semen of three buffalo bulls was sexed by a collaborating company and commercially distributed in 0.25 mL straws with a total of 2 million sexed spermatozoa. Pregnancy rates were first assessed at Day 28 following AI, and rechecked at Day 45 by ultrasound. Pregnancy rates were nonsignificantly different between animals inseminated with sexed or nonsexed semen: 80/206 (38.8%) and 40/106 (37.7%), respectively (P = 0.85). However, site of insemination of sexed semen affected pregnancy rate significantly as higher pregnancy rates were obtained when sexed semen was deposited into the body rather than the horn of the uterus: 46/101 (45.5%) and 34/105 (32.3%), respectively (P = 0.05). In conclusion, the use of sexed semen in buffalo heifers gave satisfactory and similar pregnancy rates when compared with conventional nonsexed semen. Deposition of sexed semen into the body of the uterus, however, increased pregnancy rates significantly.     

Comparison of prostaglandin- and progesterone-based protocols for timed artificial insemination in sheep

The objective was to compare the reproductive performance of a new PGF_2α-based timed artificial insemination (TAI) protocol in sheep (Synchrovine®: two doses of PGF_2α, 7 d apart) to a traditional progesterone-eCG (P4-eCG) protocol, considering the effects of seminal state, AI-times, and AI-pathway. Three experiments involving 1297 multiparous Australian Merino ewes were done during the physiologic breeding season (location 32 °S-57 °W). Reproductive performance was assessed as non-return rate to service 21 d after AI (NRR21d), based on detection with androgenized wethers, as well as Fertility (pregnant/inseminated ewes), Prolificacy (fetuses/pregnant ewe), and Fecundity (fetuses/inseminated ewe), which were based on transabdominal ultrasonography 50 d after TAI. In Experiment 1, Synchrovine® treated ewes TAI cervically with fresh semen at 42, 48, or 54 h had similar NRR21d (0.51, 0.46, 0.57), Fertility (0.27, 0.31, 0.26), and Fecundity (0.29, 0.32, 0.27), all of which were lower (P < 0.05) than in a control P4-eCG group inseminated at 54 h (0.61, 0.48, 0.52, NRR21d, Fertility and Fecundity respectively). In Experiment 2, using chilled semen and cervical TAI, Synchrovine® treated ewes inseminated at 42 h yielded lower (P < 0.05) NRR21d, Fertility and Fecundity (0.28, 0.06, 0.06) compared to 48 (0.43, 0.24, 0.24) and 54 h (0.44, 0.22, 0.23). In Experiment 3 with chilled semen, Synchrovine® treated ewes TAI into the cervix at 51 or 57 h were similar in NRR21d (0.16 vs 0.20), Fertility (0.12 vs 0.14), and Fecundity (0.12 vs 0.15), respectively; but lower (P < 0.05) than P4-eCG treated ewes TAI at 54 h (0.34, 0.28, and 0.33 for NRR21d, Fertility and Fecundity respectively). Synchrovine® treated ewes intrauterine TAI at 51 or 57 h yielded similar NRR21d (0.51 vs 0.58), Fertility (0.43 vs 0.51), and Fecundity (0.45 vs 0.56) respectively, but lower (P < 0.05) results compared to P4-eCG treated ewes (0.75, 0.71, and 0.88 for NRR21d, Fertility and Fecundity respectively). In conclusion, AI-time in Synchrovine® treated ewes with fresh semen might be extended (42 to 54 h after the second PGF_2α), but should be delayed to 48-54 h with chilled semen and cervical AI. Independent of the seminal state, AI-time or AI-pathway, Synchrovine® yielded lower reproductive results than a conventional P4-eCG protocol.     

Ubiquitous distribution of phosphatidylinositol phosphate synthase and archaetidylinositol phosphate synthase in Bacteria and Archaea,which contain inositol phospholipid

In Eukarya, phosphatidylinositol (PI) is biosynthesized from CDP-diacylglycerol (CDP-DAG) and inositol. In Archaea and Bacteria, on the other hand, we found a novel inositol phospholipid biosynthetic pathway. The precursors, inositol 1-phosphate, CDP-archaeol (CDP-ArOH), and CDP-DAG, form archaetidylinositol phosphate (AIP) and phosphatidylinositol phosphate (PIP) as intermediates. These intermediates are dephosphorylated to synthesize archaetidylinositol (AI) and PI. To date, the activities of the key enzymes (AIP synthase, PIP synthase) have been confirmed in only three genera (two archaeal genera, Methanothermobacter and Pyrococcus, and one bacterial genus, Mycobacterium). In the present study, we demonstrated that this novel biosynthetic pathway is universal in both Archaea and Bacteria, which contain inositol phospholipid, and elucidate the specificity of PIP synthase and AIP synthase for lipid substrates. PIP and AIP synthase activity were confirmed in all recombinant cells transformed with the respective gene constructs for four bacterial species (Streptomyces avermitilis, Propionibacterium acnes, Corynebacterium glutamicum, and Rhodococcus equi) and two archaeal species (Aeropyrum pernix and Sulfolobus solfataricus). Inositol was not incorporated. CDP-ArOH was used as the substrate for PIP synthase in Bacteria, and CDP-DAG was used as the substrate for AIP synthase in Archaea, despite their fundamentally different structures. PI synthase activity was observed in two eukaryotic species, Saccharomyces cerevisiae and Homo sapiens; however, inositol 1-phosphate was not incorporated. In Eukarya, the only pathway converts free inositol and CDP-DAG directly into PI. Phylogenic analysis of PIP synthase, AIP synthase, and PI synthase revealed that they are closely related enzymes.     

Genome-wide detection of allelic gene expression in hepatocellular carcinoma cells using a human exome SNP chip

Allelic variations in gene expression influence many biological responses and cause phenotypic variations in humans. In this study, Illumina Human Exome BeadChips containing more than 240,000 single nucleotide polymorphisms (SNPs) were used to identify changes in allelic gene expression in hepatocellular carcinoma cells following lipopolysaccharide (LPS) stimulation. We found 17 monoallelically expressed genes, 58 allelic imbalanced genes, and 7 genes showing allele substitution. In addition, we also detected 33 differentially expressed genes following LPS treatment in vitro using these human exome SNP chips. However, alterations in allelic gene expression following LPS treatment were detected in only three genes (MLXIPL, TNC, and MX2), which were observed in one cell line sample only, indicating that changes in allelic gene expression following LPS stimulation of liver cells are rare events. Among a total of 75 genes showing allelic expression in hepatocellular carcinoma cells, either monoallelic or imbalanced, 43 genes (57.33%) had expression quantitative trait loci (eQTL) data, indicating that high-density exome SNP chips are useful and reliable for studying allelic gene expression. Furthermore, most genes showing allelic expression were regulated by cis-acting mechanisms and were also significantly associated with several human diseases. Overall, our study provides a better understanding of allele-specific gene expression in hepatocellular carcinoma cells with and without LPS stimulation and potential clues for the cause of human disease due to alterations in allelic gene expression.     

胸部CT结合AI诊断系统对疑似肺结节患者的诊断及对结节类型的评估价值

摘要 目的：探讨胸部CT结合AI诊断系统对疑似肺结节患者的诊断及对结节类型的评估价值。方法：选取2019年12月-2020年12月在我院进行CT检查的358例疑似肺结节患者,将其按照随机数字表法分为两组：对照组（放射科医生根据CT扫描结果,通过人工阅片分析记录检出结节数量和影像特征）,观察组（将CT扫描结果导入AI辅助诊断系统,经AI运算得到结节检出数量和影像特征）。AI辅助系统IMsight用于肺结节的图像分析和自动检测。通过组织病理学确定结节的良恶性。绘制受试者工作特征曲线（ROC）曲线以评估AI和CT结合图像的诊断价值。结果：病理结果最后确诊结节数量736个,恶性结节139个（18.89 %）,良性结节597个（81.11 %）。观察组诊断结节数量717个,检出率97.42%,对照组诊断出结节数量603个,检出率81.93 %。观察组较对照组的结节检出率、阳性检出率升高（P<0.05）,漏检率和假阴性率均显著降低（P<0.05）。当结节小于10 mm时,观察组较对照组的检出率升高（P<0.05）,观察组较对照组对磨玻璃密度结节和实性结节检出率升高（P<0.05）,观察组较对照组位于胸膜结节检出率升高（P<0.05）。观察组较对照组AUC（P<0.05）,表明AI系统下的结节检出准确率高。ROC曲线显示观察组的敏感性和特异性分别为88.39%和89.68 %,对照组的敏感性和特异性分别为75.24 %和82.34 %,观察组较对照组的ROC曲线敏感性和特异性升高（P<0.05）。结论：AI辅助诊断系统可有效提高肺结节的检出率,减少误检率及漏检率,值得在肺结节CT检测中应用推广。