Description: ATP-binding cassette transporter A1 (ABCA1) and CD36, type B scavenger receptor, function as the key mediators of macrophages cholesterol efflux and intake, respectively. However, their contribution to development of foam cells still remains uncertain. We here examined the effects of increased oxidized low-density lipoprotein (oxLDL) loading on the ABCA1 and CD36 expression, and lipid accumulation in THP-1 macrophages. The cultured THP-1 macrophages were treated with different copper-oxLDL concentrations. The intracellular lipid contents and cholesterol efflux were measured, and the ABCA1 and CD36 expression were assessed. We found that expression of ABCA1 and CD36 were coordinately induced upon low to moderate doses of oxLDL loading. However, higher doses of oxLDL stimulation resulted in the imbalanced expression of ABCA1 and CD36 proteins with more preferentially suppressed ABCA1 protein, attenuated cholesterol efflux and development of THP-1 derived foam cells. The PPAR- expression was remarkably induced, and PPAR- agonist, pioglitazone, significantly promoted the ABCA1 and CD36 expression. Additionally, ABCA1 and CD36 proteins were strong colocalized in THP-1 macrophages membrane. In conclusion, the more preferentially suppressed ABCA1 expression as compared with CD36 at higher doses of oxLDL stimulation may be the initiator for the formation of macrophage-derived foam cells.

Description: Background Recent studies have revealed that miR-196a is upregulated in glioblastoma multiforme (GBM) and that it correlates with the clinical outcome of patients with GBM. However, its potential regulatory mechanisms in GBM have never been reported. Methods We used quantitative real-time PCR to assess miR-196a expression levels in 132 GBM specimens in a single institution. Oncogenic capability of miR-196a was detected by apoptosis and proliferation assays in U87MG and T98G cells. Immunohistochemistry was used to determine the expression of IBα in GBM tissues, and a luciferase reporter assay was carried out to confirm whether IBα is a direct target of miR-196a. In vivo, xenograft tumors were examined for an antiglioma effect of miR-196a inhibitors. Results We present for the first time evidence that miR-196a could directly interact with IBα 3'-UTR to suppress IBα expression and subsequently promote activation of NF-B, consequently promoting proliferation of and suppressing apoptosis in GBM cells both in vitro and in vivo. Our study confirmed that miR-196a was upregulated in GBM specimens and that high levels of miR-196a were significantly correlated with poor outcome in a large cohort of GBM patients. Our data from human tumor xenografts in nude mice treated with miR-196 inhibitors demonstrated that inhibition of miR-196a could ameliorate tumor growth in vivo. Conclusions MiR-196a exerts its oncogenic effect in GBM by inhibiting IBα both in vitro and in vivo. Our findings provide new insights into the pathogenesis of GBM and indicate that miR-196a may predict clinical outcome of GBM patients and serve as a new therapeutic target for GBM.

Description: Retinitis pigmentosa (RP), a disease characterized by progressive loss of photoreceptors, exhibits significant genetic heterogeneity. Several genes associated with U4/U6–U5 triple small nuclear ribonucleoprotein (tri-snRNP) complex of the spliceosome have been implicated in autosomal dominant RP (adRP). HPrp4, encoded by PRPF4 , regulates the stability of U4/U6 di-snRNP, which is essential for continuous splicing. Here, we identified two heterozygous variants in PRPF4 , including c.-114_-97del in a simplex RP patient and c.C944T (p.Pro315Leu), which co-segregates with disease phenotype in a family with adRP. Both variants were absent in 400 unrelated controls. The c.-114_-97del, predicted to affect two transcription factor binding sites, was shown to down-regulate the promoter activity of PRPF4 by a luciferase assay, and was associated with a significant reduction of PRPF4 expression in the blood cells of the patient. In fibroblasts from an affected individual with the p.Pro315Leu variant, the expression levels of several tri-snRNP components, including PRPF4 itself, were up-regulated, with altered expression pattern of SC35, a spliceosome marker. The same alterations were also observed in cells over expressing hPrp4 Pro315Leu , suggesting that they arose as a compensatory response to a compromised splicing mechanism caused by hPrp4 dysfunction. Further, over expression of hPrp4 Pro315Leu , but not hPrp4 WT , triggered systemic deformities in wild-type zebrafish embryos with the retina primarily affected, and dramatically augmented death rates in morphant embryos, in which orthologous zebrafish prpf4 gene was silenced. We conclude that mutations of PRPF4 cause RP via haploinsufficiency and dominant-negative effects, and establish PRPF4 as a new U4/U6–U5 snRNP component associated with adRP.

Description: Long intergenic noncoding RNAs (lincRNAs) are long noncoding transcripts (〉200 nt) from the intergenic regions of annotated protein-coding genes. We report here that the lincRNA gene lincRNA-Tnfaip3 , located at mouse chromosome 10 proximal to the tumor necrosis factor α-induced protein 3 ( Tnfaip3 ) gene, is an early-primary response gene controlled by nuclear factor-B (NF-B) signaling in murine macrophages. Functionally, lincRNA- Tnfaip3 appears to mediate both the activation and repression of distinct classes of inflammatory genes in macrophages. Specifically, induction of lincRNA-Tnfaip3 is required for the transactivation of NF-B-regulated inflammatory genes in response to bacterial LPSs stimulation. LincRNA-Tnfaip3 physically interacts with the high-mobility group box 1 (Hmgb1), assembling a NF-B/Hmgb1/lincRNA-Tnfaip3 complex in macrophages after LPS stimulation. This resultant NF-B/Hmgb1/lincRNA-Tnfaip3 complex can modulate Hmgb1-associated histone modifications and, ultimately, transactivation of inflammatory genes in mouse macrophages in response to microbial challenge. Therefore, our data indicate a new regulatory role of NF-B-induced lincRNA-Tnfaip3 to act as a coactivator of NF-B for the transcription of inflammatory genes in innate immune cells through modulation of epigenetic chromatin remodeling.—Ma, S., Ming, Z., Gong, A.-Y., Wang, Y., Chen, X., Hu, G., Zhou, R., Shibata, A., Swanson, P. C., Chen, X.-M. A long noncoding RNA, LincRNA-Tnfaip3, acts as a coregulator of NF-B to modulate inflammatory gene transcription in mouse macrophages.

Description: Siglecs are sialic acid-binding Ig-like lectins that recognize sialoglycans via amino-terminal V-set domains. CD33-related Siglecs (CD33rSiglecs) on innate immune cells recognize endogenous sialoglycans as "self-associated molecular patterns" (SAMPs), dampening immune responses via cytosolic immunoreceptor tyrosine-based inhibition motifs that recruit tyrosine phosphatases. However, sialic acid-expressing pathogens subvert this mechanism through molecular mimicry. Meanwhile, endogenous host SAMPs must continually evolve to evade other pathogens that exploit sialic acids as invasion targets. We hypothesized that these opposing selection forces have accelerated CD33rSiglec evolution. We address this by comparative analysis of major CD33rSiglec (Siglec-3, Siglec-5, and Siglec-9) orthologs in humans, chimpanzees, and baboons. Recombinant soluble molecules displaying ligand-binding domains show marked quantitative and qualitative interspecies differences in interactions with strains of the sialylated pathogen, group B Streptococcus , and with sialoglycans presented as gangliosides or in the form of sialoglycan microarrays, including variations such as N -glycolyl and O -acetyl groups. Primate Siglecs also show quantitative and qualitative intra- and interspecies variations in expression patterns on leukocytes, both in circulation and in tissues. Taken together our data explain why the CD33rSiglec-encoding gene cluster is undergoing rapid evolution via multiple mechanisms, driven by the need to maintain self-recognition by innate immune cells, while escaping 2 distinct mechanisms of pathogen subversion.—Padler-Karavani, V., Hurtado-Ziola, N., Chang, Y.-C., Sonnenburg, J. L., Ronaghy, A., Yu, H., Verhagen, A., Nizet, V., Chen, X., Varki, N., Varki, A., Angata, T. Rapid evolution of binding specificities and expression patterns of inhibitory CD33-related Siglecs in primates.

Description: The successful synthesis of a transcript by RNA polymerase II (RNAPII) is a multistage process with distinct rate-limiting steps that can vary depending on the particular gene. A growing number of genes in a variety of organisms are regulated at steps after the recruitment of RNAPII. The best-characterized Saccharomyces cerevisiae gene regulated in this manner is CYC1 . This gene has high occupancy of RNAPII under non-inducing conditions, defining it as a poised gene. Here, we find that subunits of the head module of Mediator, Med18 and Med20, and Med19 are required for activation of transcription at the CYC1 promoter in response to environmental cues. These subunits of Mediator are required at the preloaded promoter for normal levels of recruitment and activity of the general transcription factor TFIIH. Strikingly, these Mediator components are dispensable for activation by the same activator at a different gene, which lacks a preloaded polymerase in the promoter region. Based on these results and other studies, we speculate that Mediator plays an essential role in triggering an inactive polymerase at CYC1 into a productively elongating form.

Description: Angular fluctuations of the near-infrared background (NIRB) intensity are observed up to scales 1°. Their interpretation is challenging as even after removing the contribution from detected sources, the residual signal is 〉10 times higher than expected from distant galaxies below the detection limit and first stars. We propose here a novel interpretation in which early, intermediate-mass, accreting direct collapse black holes (DCBHs), which are too faint to be detected individually in current surveys, could explain the observed fluctuations. We find that a population of highly obscured ( N H 10 25 cm –2 ) DCBHs formed in metal-free haloes with virial temperature 10 4  K at z 12 can explain the observed level 10 –3 (nW m –2 sr –1 ) 2 of the 3.6 and 4.5 μm fluctuations on scales 〉100 arcsec. The signal on smaller scales is instead produced by undetected galaxies at low and intermediate redshifts. Albeit Compton-thick, at scales  〉 100 arcsec DCBHs produce a cosmic X-ray background (0.5–2 keV)-NIRB (4.5 μm) cross-correlation signal of ~=10 –11  erg s –1  cm –2 nW m –2 sr –1 slightly dependent on the specific value of the absorbing gas column ( N H 10 25 cm –2 ) adopted and in agreement with the recent measurements by Cappelluti et al. At smaller scales the cross-correlation is dominated by the emission of high-mass X-ray binaries hosted by the same low- z , undetected galaxies accounting for small-scale NIRB fluctuations. These results outline the great potential of the NIRB as a tool to investigate the nature of the first galaxies and black holes.

Description: Mutation rate is one of the most fundamental parameters in genetics and evolutionary biology because mutation rate has major impacts on the incidence of disease, the amount of genetic variation, and the rate and trajectory of evolution. Based on estimates of synonymous nucleotide diversity in Escherichia coli , a recent study claimed that the per-nucleotide mutation rate in a gene decreases with the rise of its expression level or the intensity of purifying selection and that this trend reflects adaptive risk management. Here, we demonstrate that this argument is theoretically untenable, especially in the lack of mechanisms that simultaneously tune the mutabilities of multiple genes with similar fractions of deleterious mutations. Analyzing published genome sequences of E. coli mutation accumulation lines, we show that mutation rates are actually higher in more highly expressed genes, similar to previous genome-wide observations in Salmonella typhimurium , Saccharomyces cerevisiae , and the human germline. These general patterns likely arise from transcription-associated mutagenesis that exceeds transcription-coupled repair.