STAT3-Mediated Promoter-Enhancer Interaction Up-Regulates Inhibitor of DNA Binding 1 (ID1) to Promote Colon Cancer Progression

BACKGROUND

High expression of inhibitor of DNA binding 1 (ID1) correlates with poor prognosis in colorectal cancer (CRC). Aberrant enhancer activation in regulating ID1 transcription is limited.

METHODS

Immunohistochemistry (IHC), quantitative RT-PCR (RT-qPCR) and Western blotting (WB) were used to determine the expression of ID1. CRISPR-Cas9 was used to generate ID1 or enhancer E1 knockout cell lines. Dual-luciferase reporter assay, chromosome conformation capture assay and ChIP-qPCR were used to determine the active enhancers of ID1. Cell Counting Kit 8, colony-forming, transwell assays and tumorigenicity in nude mice were used to investigate the biological functions of ID1 and enhancer E1.

RESULTS

Human CRC tissues and cell lines expressed a higher level of ID1 than normal controls. ID1 promoted CRC cell proliferation and colony formation. Enhancer E1 actively regulated ID1 promoter activity. Signal transducer and activator of transcription 3 (STAT3) bound to ID1 promoter and enhancer E1 to regulate their activity. The inhibitor of STAT3 Stattic attenuated ID1 promoter and enhancer E1 activity and the expression of ID1. Enhancer E1 knockout down-regulated ID1 expression level and cell proliferation in vitro and in vivo.

CONCLUSIONS

Enhancer E1 is positively regulated by STAT3 and contributes to the regulation of ID1 to promote CRC cell progression and might be a potential target for anti-CRC drug studies.

Comprehensive landscape of epigenetic-dysregulated lncRNAs reveals a profound role of enhancers in carcinogenesis in BC subtypes

Aberrant expression of long non-coding RNAs (lncRNA) is associated with altered DNA methylation and histone modifications during carcinogenesis. However, identifying epigenetically dysregulated lncRNAs and characterizing their functional mechanisms in different cancer subtypes are still major challenges for cancer studies. In this study, we systematically analyzed the epigenetic alterations of lncRNAs at important regulatory elements in three breast cancer subtypes. We identified 87, 691, and 1,197 epigenetically dysregulated lncRNAs in luminal, basal, and claudin-low subtypes of breast cancer, respectively. The landscape of epigenetically dysregulated lncRNAs at enhancer elements revealed that epigenetic changes of the majority of lncRNAs occurred in a subtype-specific manner and contributed to subtype-specific biological functions. We identified six acetylation of lysine 27 on histone H3 (H3K27ac)-dysregulated lncRNAs and three DNA methylation-dysregulated lncRNAs (CTC-303L1.2, RP11-738B7.1, and SLC26A4-AS1) as prognostic biomarkers of basal subtype. These lncRNAs were involved in immune response-related biological functions. Treatment of the basal breast cancer cell line MDA-MB-468 with CREBBP/EP300 bromodomain inhibitors downregulated H3K27 acetylation levels and caused a decrease in the expression of five H3K27ac-dysregulated lncRNAs (LINC00393, KB-1836B5.1, RP1-140K8.5, AC005162.1, and AC020916.2) and inhibition of the growth of breast cancer cells. One epigenetically dysregulated lncRNA (LINC01983) and four lncRNA regulators (UCA1, RP11-221J22.2, RP11-221J22.1, and RP1-212P9.3) were identified as prognostic biomarkers of the luminal molecular subtype of breast cancer by controlling the tumor necrosis factor (TNF) signaling pathway, T helper (Th)17 cell differentiation, and T cell migration. Finally, our results highlighted a profound role of enhancer-related H3K27ac-dysregulated lncRNAs, DNA methylation-dysregulated lncRNAs, and lncRNA regulators in breast cancer subtype carcinogenesis and their potential prognostic value.

LncTarD: a manually-curated database of experimentally-supported functional lncRNA-target regulations in human diseases

Long non-coding RNAs (lncRNAs) are associated with human diseases. Although lncRNA–disease associations have received significant attention, no online repository is available to collect lncRNA-mediated regulatory mechanisms, key downstream targets, and important biological functions driven by disease-related lncRNAs in human diseases. We thus developed LncTarD (http://biocc.hrbmu.edu.cn/LncTarD/ or http://bio-bigdata.hrbmu.edu.cn/LncTarD), a manually-curated database that provides a comprehensive resource of key lncRNA–target regulations, lncRNA-influenced functions, and lncRNA-mediated regulatory mechanisms in human diseases. LncTarD offers (i) 2822 key lncRNA–target regulations involving 475 lncRNAs and 1039 targets associated with 177 human diseases; (ii) 1613 experimentally-supported functional regulations and 1209 expression associations in human diseases; (iii) important biological functions driven by disease-related lncRNAs in human diseases; (iv) lncRNA–target regulations responsible for drug resistance or sensitivity in human diseases and (v) lncRNA microarray, lncRNA sequence data and transcriptome data of an 11 373 pan-cancer patient cohort from TCGA to help characterize the functional dynamics of these lncRNA–target regulations. LncTarD also provides a user-friendly interface to conveniently browse, search, and download data. LncTarD will be a useful resource platform for the further understanding of functions and molecular mechanisms of lncRNA deregulation in human disease, which will help to identify novel and sensitive biomarkers and therapeutic targets.

Towards a table-top microscope for nanoscale magnetic imaging using picosecond thermal gradients

Research advancement in magnetoelectronics is challenged by the lack of a table-top magnetic measurement technique with the simultaneous temporal and spatial resolution necessary for characterizing magnetization dynamics in devices of interest, such as magnetic memory and spin torque oscillators. Although magneto-optical microscopy provides superb temporal resolution, its spatial resolution is fundamentally limited by optical diffraction. To address this challenge, we study heat rather than light as a vehicle to stroboscopically transduce a local magnetic moment into an electrical signal while retaining picosecond temporal resolution. Using this concept, we demonstrate spatiotemporal magnetic microscopy using the time-resolved anomalous Nernst effect (TRANE). Experimentally and with supporting numerical calculations, we find that TRANE microscopy has temporal resolution below 30 ps and spatial resolution determined by the area of thermal excitation. Based on these findings, we suggest a route to exceed the limits imposed by far-field optical diffraction.

Mobile elements carrying ermF and tetQ genes in gram-positive and gram-negative bacteria

Bacteroides spp. conjugative transposon Tn5030 is 150 kb which includes a 43 kb characterized region containing a number of defined genes and an open reading frame (ORF). The 43 kb region is organized with the ORF1 immediately upstream from the ermF gene, coding for an rRNA methylase, then an unknown 20 kb region downstream followed by the tetQ gene (coding for a ribosomal protection protein) then the rteA and rteB genes. The role of ORF1 is unclear; rteA is a putative sensor and rteB a regulator. Thirty-seven (62%) of 60 isolates, representing one gram-positive anaerobic and 13 gram-negative anaerobic species, co-transferred the ermFand tetQ genes to an unrelated Enterococcus faecalis recipient. We used the polymerase chain reaction to show the linkage between ORF1, ermF, tetQ, rteA and rteB. Our data suggest that the ORF1 gene product may participate in the transfer of the ermF gene with or without the ORF1-rteB region and has homology to bacterial transposases. Isolates that co-transferred the ermF and tetQ genes carried and transferred the rteB gene, suggesting that the rteB gene product may be important in transfer of the 43 kb ORF1-rteB region to E. faecalis. The rteB gene product is not required when ermF is transferred independently of tetQ.

Characterization of ciliary activity in distal Fallopian tube biopsies of women with obstructive tubal infertility

Biopsy specimens were obtained from the distal end of the Fallopian tubes of 62 women with tubal infertility and examined by light and electron microscopy. Ciliary beat frequency (CBF) measurements were obtained using laser light spectroscopy. Neither demographic nor behavioural characteristics nor serological evidence of past chlamydial infection were associated with CBF measurements. In contrast, CBF were significantly lower (P < 0.05) in tissues with oedema compared to tissues without oedema (6.7 versus 12.9) and in tissues with erythema compared to tissues without erythema (9.2 versus 13.7). Furthermore, CBF measurements did vary by chlamydial serotype pattern, with lower values observed among the tissues of women with antibodies to serotype C or E (without D) as compared to the tissues of women with other serotypes (P < 0.04). However, these data must be interpreted with caution as the numbers of subjects with chlamydial antibodies to serotype C (n = 3) or E without D (n = 5) were few in number and serotyping of IgG antibodies in blood is not as accurate as it is in bacterial isolates. Confirmation of the suggested association between chlamydial serotype and risk of adverse sequelae could indicate potential new avenues for vaccine research.

Study on Haemophilus influenzae type b diseases in China: the past, present and future

Meningitis caused by Haemophilus influenzae type b (Hib) is a common and serious disease for which there now are WHO-certified vaccines that are recommended for universal infant immunization in North America and European countries. If these vaccines are to be recommended in Asia, it is necessary to know the incidence, age distribution and clinical outcome of Hib meningitis and other systemic infections in this region. Data on Hib disease in China are scanty. Hib meningitis was common during the 1950s in China, accounting for up to 16% of all of pyogenic meningitis (up to 38% of cases were caused by unknown pathogens), despite severe epidemics of meningococcal meningitis during that period. Since 1989 we have conducted hospital- and community-based etiologic and epidemiologic studies of bacterial meningitis. Hib accounts for 30 to 50% of bacterial meningitis in China. The incidence of Hib meningitis in Hefei City was 10.4 per 100000 children <5 years, a result relatively lower than in the West but higher than the rate of 2.7 found in a retrospective study in Hong Kong. Pneumonia is the primary cause of death for Chinese children. From 1991 to 1993 the average mortality of children<5 years because of pneumonia was 1563.2 per 100000. To achieve the goal of reducing the death rate of children by one-third by the year 2000, greater efforts should be made to reduce the mortality of children with pneumonia. Our preliminary study showed that about one-fourth to one-third of cases of pneumonia in Chinese children might be caused by Hib. Therefore Hib vaccination for infants and children in China might be an effective and valuable procedure to achieve the goal.

[Study of adsorptive voltammetry for adrenaline on carbon paste electrode]

Adrenaline is determined by adsorptive voltammetry using a carbon paste electrode in a base solution of 0.5 mol.L-1 H2SO4. The peak potential of anode is 0.58 V (vs. SCE). There is a good linear relationship between the peak current and the concentration of adrenaline in the range of 5.0 x 10(-9)-1.0 x 10(-4) mol.L-1. The detection limit of the method is 2.5 x 10(-9) mol.L-1. The recovery is 93.75%-103.33%, and the relative standard deviation is 3.1% (n = 12). The adrenaline hydrochloride injection has been determined with good results by this method. The possible reaction mechanism is discussed. The electrode reaction of adrenaline is irreversible process with two electrons and two protons on the carbon paste electrode.

[Pediatric Haemophilus influenzae type b meninngitis in Hefei city: an epidemiologic study]

OBJECTIVE

To obtain epidemiologic information about Hib meningitis from Hefei.

METHODS

Data were collected from 1990 to 1992 by a coordinative group including 13 hospitals. All children with a clinical diagnosis of acute bacterial meningitis were enrolled and specimens were taken for etiologic studies. CSF and blood were tested by standard bacteriologic technique. CSF, blood and concentrated urine were tested directly for detecting antigen by CIE. The data were analysed by epidemiologic methods.

RESULTS

Of 60 cases of bacterial meningitis clinically diagnosed, 31 (51.7%) were CIE positive for Hib antigen. Only 3 cases of CSF culture were positive for Hib. The annual incidence of Hib meningitis in Hefei was culculated as 4.81/100,000 children younger than 15 years and 10.66/100,000 children younger than 5 years. The case fatality rate was 9.7%. 21.4% of survivors suffered from neurological or psychological problems.

CONCLUSIONS

Using antigen detection combined with bacterial culture, we could make etiologic diagnosis in 90% of the cases. Hib is the most common cause of bacterial meningitis, but the incidence is much lower than in most parts of the world.

Distribution and mobility of the tetracycline resistance determinant tetQ

We tested 34 American Type Culture Collection (ATCC) and 168 clinical bacterial isolates, from the human urogenital and oral tracts and streptococci isolated from cows with mastitis, for the presence of the tetQ gene using a polymerase chain reaction (PCR) assay and DNA-DNA hybridization. The identities of PCR products were confirmed by Southern blot hybridization of whole-cell DNA. Eleven of the ATCC strains were positive for tetQ, including five Bacteroides spp., five Prevotella spp. and a single isolate of Mitsuokella multiacidus. Twenty-eight (29%) of the 95 clinical Gram-negative isolates carried the tetQ gene, while eight (11%) of the 73 clinical Gram-positive isolates carried the tetQ gene. This is the first description of tetQ in Gram-positive species. All isolates except one Peptostreptococcus sp. carried tetQ integrated into the chromosome. The tetQ gene could be transferred from Prevotella bivia, Bacteroides ovatus, Bacteroides fragilis, Bacteroides vulgatus and Bacteroides distasonis into an Enterococcus faecalis recipient at frequencies of 10(-7)-10(-9) per recipient. In contrast, tetQ failed to transfer from two isolates of Prevotella intermedia, two isolates of Porphyromonas gingivalis, one isolate of Mobiluncus curtisii and one isolate of Peptostreptococcus sp. The latter two are Gram-positive species. The PCR assay was used to screen 198 proteinase K-treated biopsies of prostate, periprostate and bladder from 84 men with prostatitis. Thirty-four (40%) of the patients had one or more positive samples, suggesting that the PCR assay could be of value in screening patient material directly for the presence of bacteria.

Acute bacterial meningitis in children in Hefei, China 1990-1992

OBJECTIVE

To obtain etiologic and epidemiologic information about bacterial meningitis, especially the H influenza type B (Hib), from a medium-sized city, Hefei, China.

METHODS

Data were collected prospectively over 3 years, from 1990 to 1992 by a well-organized group including 13 hospitals. All children with a clinical diagnosis of acute bacterial meningitis were enrolled and the specimens were taken for the etiologic studies. CSF and blood were tested by standard bacteriologic technique. CSF, blood and concentrated urine were tested directly for detection of antigen by countercurrent immuno-electrophoresis (CIE). Data were analyzed by epidemiologic methods.

RESULTS

Bacterial culture and CSF Gram's staining were positive only in 13.3% and 11.7%, respectively. Bacterial antigen detection was positive in up to 90% by CIE which was more sensitive than bacterial culture (chi 2 = 67.7, P < 0.005). The annual incidence of acute bacterial meningitis in the city is calculated as 9.3 cases/100,000 children from 1 month to 15 years of age and 19.2 cases/100,000 children from 1 month to 5 years of age. Hib meningitis accounted for 51.7%, N. meningitis (Nm) for 38.3%, and S. pneumoniae (Sp) for 8.3%. There was no significant seasonal variation. Of the patients, 76.7% were children under 5 years of age, and 51.7% under 1 year of age. The case fatality rate was 11.7% for all bacterial meningitis, 9.7% for Hib, 17.4% for Nm and 20% for Sp. A total of 22.6% of survivors suffered from neurological or psychological problems.

CONCLUSIONS

Using antigen detection combined with bacterial culture, we could make an etiologic diagnosis in up to 90% of the patients in this group. Hib, Nm and Sp were the predominant pathogens, which was similar to the findings in other countries. Hib was the most common cause of bacterial meningitis, but the incidence was much lower than in most parts of the world.

Evaluation of the detection limits of PCR for identification of Mycoplasma pneumoniae in clinical samples

The detection limits of the polymerase chain reaction (PCR) for Mycoplasma pneumoniae were determined using specimens from persons known to have had M. pneumoniae pneumonia. Four primers were selected from the known sequence of the P1 gene. The primer pair (P1-178 and P1-809) which generates a 631 fragment gave the lowest detection limit. Nineteen of 21 throat swabs, which contained between 0.06 and 2 colony-forming units (CFU) per microlitre, from culture positive patients, were positive by PCR. The fact that M. pneumoniae grows in broth culture in spherules causes problems for determining the number of CFU detected in PCR. Filtering broth cultures through a 0.6 micron polycarbonate filter increased the number of CFUs two-to-ten-fold compared to unfiltered cultures. The lysis method needed to assay throat swabs differed from that necessary for broth cultures in that proteinase K treatment for 18 h increased the detection limit 10- to 100-fold when compared to NaOH digestion.

Cytoplasmic and nuclear signaling pathways of V1-vascular vasopressin receptors

We studied the cytoplasmic and nuclear signaling pathways of V1-vascular AVP receptors of human platelets, primary cultures of renal glomerular mesangial cells, and established cultures of the A7r5 aortic smooth muscle cell line. The immediate transmembrane signals are triggered by the formation of ligand-receptor complexes as illustrated by binding experiments with [3H]AVP (Kd = 2.50 nM), d(CH2)5Tyr(Me)AVP (Kd = 0.62 nM), the linear V1 antagonist phenylacetyl-D-Tyr(Et)-Phe-Val-Asn-Lys-Pro-[125I]Tyr-NH2 (Kd = 1.42 nM) or by fluorescence experiments with linear antagonists like phenylacetyl-D-Tyr(Et)-Phe-Gln-Asn-Lys-Pro-Arg-NH2 coupled to biotin and made fluorescent by labeling with tetramethylrhodamine-avidin. We used several approaches (radioreceptor binding, radioactive labeling, autoradiographic, enzymatic, photoaffinity labeling, and immunoblotting procedures) to identify the guanine nucleotide regulatory protein coupled to V1-vascular vasopressin receptors. AVP-stimulated GTPase activity of human platelet membranes was blocked by pretreatment with antibodies specific for the C-terminal of the newly described Gq alpha protein. In the presence of MgCl2, AVP increased labeling by the photoreactive GTP analog [alpha-32P]azidoanilido GTP of a platelet membrane protein of apparent molecular mass of 42 kDa. AVP effect was reversed by the specific V1-vascular antagonist d(CH2)5Tyr(Me)AVP and labeling was completely abolished by GTP gamma s.(ABSTRACT TRUNCATED AT 250 WORDS)