Comprehensive analysis of the m6A-related molecular patterns and diagnostic biomarkers in osteoporosis

BACKGROUND

N6-methyladenosine (m6A) modification is a critical epigenetic modification in eukaryotes and involves several biological processes and occurrences of diseases. However, the roles and regulatory mechanisms of m6A regulators in osteoporosis (OP) remain unclear. Thus, the purpose of this study is to explore the roles and mechanisms of m6A regulators in OP.

METHODS

The mRNA and microRNA (miRNA) expression profiles were respectively obtained from GSE56815, GSE7158, and GSE93883 datasets in Gene Expression Omnibus (GEO). The differential expression of 21 m6A regulators between high-bone mineral density (BMD) and low-BMD women was identified. Then, a consensus clustering of low-BMD women was performed based on differentially expressed (DE)-m6A regulators. The m6A-related differentially expressed genes (DEGs), the differentially expressed miRNAs (DE-miRNAs), and biological functions were investigated. Moreover, a weighted gene co-expression network analysis (WGCNA) was constructed to identify the OP-related hub modules, hub genes, and the functional pathways. Then, an m6A regulator-target-pathway network and the competing endogenous RNA (ceRNA) network in key modules were constructed. A least absolute shrinkage and selection operation (LASSO) Cox regression model and a Support Vector Machine-Recursive Feature Elimination (SVM-RFE) model were constructed to identify the candidate genes for OP prediction. The receiver operator characteristic (ROC) curves were used to validate the performances of predictive models and candidate genes.

RESULTS

A total of 10,520 DEGs, 13 DE-m6A regulators, and 506 DE-miRNAs between high-BMD and low-BMD women were identified. Two m6A-related subclusters with 13 DE-m6A regulators were classified for OP. There were 5,260 m6A-related DEGs identified between two m6A-related subclusters, the PI3K-Akt, MAPK, and immune-related pathways, and bone metabolism was mainly enriched in cluster 2. Cell cycle-related pathways, RNA methylation, and cell death-related pathways were significantly involved in cluster 1. Five modules were identified as key modules based on WGCNA, and an m6A regulator-target gene-pathway network and the ceRNA network were constructed in module brown. Moreover, three m6A regulators (FTO, YTHDF2, and CBLL1) were selected as the candidate genes for OP.

CONCLUSION

M6A regulators play an important role in the occurrences and diagnosis of OP.

Detection of hand-foot-mouth disease and its spatial-temporal Epidemiological characteristics with GIS platform

The aim of this study is to investigate the main category of hand-foot-mouth (HFM) virus and analyze the distribution characteristics and susceptible population of HFM disease in China. Infants who have had HFM disease for less than 7 days were selected from the First Affiliated Hospital of Guangxi Medical University, Guangxi, China. Various specimens were collected from the infants, and EV71 and CA16 nucleic acid detections were performed using fluorescence quantitative assay. The positive results of the specimens were compared to determine the components of the pathogen. Moreover, the data of the target cases were analyzed based on Geographic Information System (GIS) to obtain the spatial-temporal epidemiological features of HFM disease in China. The detection rate of HFM virus in the throat swab, feces, bleb fluid and cerebrospinal fluid were 75%, 81.13%, 85.71% and 25%, respectively, indicating that the detection rate of virus in the bleb fluid was the highest. When the detection was based on more than one specimen, it was found that the positive rate was higher compared to detection based on a single specimen. The positive detection rate of EV71 in the target specimens was significantly higher than that of CA16 and mixed infection. Moreover, CA16 infection was usually accompanied by EV71 infection. As to spatial-temporal distribution, hand-foot-month disease broke out in the South of China in April, then spread to the north, and diminished in July. There was a notable difference in the number of cases between different provinces. EV71 and CA16 are the main viruses inducing HFM disease, especially EV71. Fluorescence quantitative polymerase chain reaction with high sensitivity can be used to detect the copy number of viruses, which is applicable to the early diagnosis of HFM disease. The incidence of HFM disease is notably different according to the influence of time, geographical space, gender and the living conditions of the children. Early diagnosis and treatment based on scientific methods are needed to reduce the incidence of severe diseases and avoid death.

Development and characterization of potent and specific peptide inhibitors of p60c-src protein tyrosine kinase using pseudosubstrate-based inhibitor design approach

The cytoplasmic protein p60c-src, an ubiquitous non-receptor protein tyrosine kinase (PTK) is a potential anticancer target as it is over-expressed and/or constitutively active in several cancer types. In addition, the phenotype of c-src knock-out mice is consistent with osteopetrosis, which suggests that inhibitors against this enzyme may also be therapeutic for osteoporosis. Using a known peptide substrate for c-src, MIYKYYF, as a template, we have developed a series of pseudosubstrate-based peptide inhibitors. Structure-activity relationship studies have been performed on one of these inhibitors, CIYKYYF. In a kinase assay using YIYGSFK as the substrate, CIYKYY has been demonstrated to inhibit p60c-src, with an IC50 of 0.6 microm. Further truncation has led to the determination that even the smaller peptide, CIYK, is a moderately potent inhibitor with IC50 of 15 microm. Some improvement in inhibitory potency (IC50 = 11.8 microm) has been observed with the replacement of Tyr3 in CIYK with beta-phenylalanine (beta-Phe). The tetrapeptide CI(beta-Phe)K will be used as a lead compound for future development of peptidomimetics and small molecule inhibitors that have the capacity to penetrate the plasma membrane of intact cells.

A comparison of the effect of three sedatives on esophageal sphincters in cats

BACKGROUND/AIMS

Children 5 years old and younger often require sedation for esophageal motility studies (EMS). At our institution, an intramuscular cocktail of meperidine, promethazine and chlorpromazine (MPC) has been used as the standard sedative for young children undergoing EMS. Administering the intramuscular sedative may, however, be more traumatic to the child than the procedure. Moreover, its effect on esophageal motility is not known and prolonged sedation is common. The aim of this study was to determine the effects of MPC and two orally-administered sedatives on esophageal sphincter function, using the cat model, with a goal to identify a potentially suitable orally-administered sedative for use in young children requiring sedation for EMS.

METHODS

We measured upper (UESP) and lower (LESP) esophageal sphincter pressures in 25 cats initially without sedation, and then following sedation with midazolam, chloral hydrate and MPC. The results were compared.

RESULTS

All three sedatives significantly decreased LESP compared to the control (p<0.05). Midazolam decreased LESP the most; however, the difference from the other sedatives did not reach statistical significance. All three sedatives decreased UESP, compared to control, but the differences were not statistically significant. Of the two oral sedatives, chloral hydrate had the least effect on the esophageal sphincters although its effect was not statistically different from that of midazolam.

CONCLUSIONS

Ethically appropriate studies are needed to determine which oral sedative would be most beneficial for use in sedating children undergoing esophageal motility studies. Until studies can be done, the choice between chloral hydrate and midazolam should be based on the experience and comfort of the attending physician with regard to the potential side effects of the medications.

Comparison of five PCR methods for detection of Helicobacter pylori DNA in gastric tissues

Five different PCR methods for the detection of Helicobacter pylori were evaluated. The results of this study indicate that of the five PCR methods examined, the ureC (glmM) gene PCR is the most sensitive and specific for the detection of H. pylori in gastric biopsy specimens.

A Lewis(y) epitope mimicking peptide induces anti-Lewis(y) immune responses in rabbits and mice

Lewis(y) carbohydrate antigens are abundant on the surface of many carcinomas. Mab B3 directed against this carbohydrate antigen has been used to make an immunotoxin that is very cytotoxic to cancer cells expressing the Lewis(y) antigen. Mab B3 was also used to screen a phage-displayed peptide library and identified a peptide mimicking the Lewis(y) epitope. In this report, we demonstrate that the Lewis(y) epitope-mimicking peptide induces anti-Lewis(y)immune responses in both rabbits and mice. In addition, Lewis(y) antigens induce anti-peptide immune responses. These results indicate that carbohydrate-mimicking peptides provide a novel strategy to elicit immune responses for tumor-associated carbohydrates.

Prevalence of immunoglobulin G to Helicobacter pylori among endoscopy nurses/technicians

The purpose of this study was to compare the prevalence of Helicobacter pylori (HP) seropositivity among gastroenterology nurses and technicians with that of the general population. Nurses attending the 1996 Indiana Society of Gastroenterology Nurses and Associates Spring and Fall Education Courses were asked to complete a checklist regarding employment, current symptoms, and use of universal precautions, and to have 3 ml blood drawn. These 138 blood specimens as well as 112 serum samples from generally age- and sex-matched blood donors (representing the general population) underwent qualitative HP antibody testing. Results showed that the prevalence of seropositivity for immunoglobulin G (IgG) antibody for HP among the gastroenterology nurses and technicians was 19 of 138 (13.8%), which was less than that of the blood donor control group, whose seropositivity was 20 of 112 (17.9%). However, this difference failed to reach statistical significance. Seropositivity tended to increase with age, but there was no association between clinical symptomatology and seropositivity. Likewise, there was no difference in seropositivity between nurses assisting with endoscopic procedures for more than 10 years and those assisting for less than 10 years. Although the differences were not significant, these findings refute those of an earlier study in which the researchers found 122 gastroendoscopists and endoscopy nurses significantly more likely to be positive for HP antibodies. Therefore, the findings reported here provide important information.

Discovery of a novel series of potent and selective substrate-based inhibitors of p60c-src protein tyrosine kinase: conformational and topographical constraints in peptide design

On the basis of the efficient substrate for p60c-src protein tyrosine kinase (PTK) YIYGSFK-NH2 (1) (Km = 55 microM) obtained by combinatorial methods, we have designed and synthesized a series of conformationally and topographically constrained substrate-based peptide inhibitors of this enzyme, which showed IC50 values in the low-micromolar range (1-3 microM). A "rotamer scan" was performed by introducing the four stereoisomers of beta-Me(2')Nal in the postulated interaction site of the peptide inhibitor 23(IC50 = 1.6 microM). This substitution led to selective and potent inhibitors of p60c-src PTK; however, no substantial difference in potency was observed among them. This and the results of the "stereochemical scan" performed at residues 2 and 7 of 3 (peptides 19-21), which form the disulfide bond, may suggest that the enzyme active site does not have rigid topographic requirements and thus is able to achieve important conformational changes to bind the ligand as long as the pharmacophore pattern in the inhibitor is conserved. Two new potent iodo-containing nonphosphorylatable tyrosine analogues were also incorporated into our lead inhibitory sequence 23, producing the most potent inhibitors for p60c-src PTK identified thus far in our studies. Compounds 29 and 30 exhibit IC50 values of 0.13 and 0.54 microM, respectively. Peptide 29 is 420-fold more potent than the parent peptide 1. Selectivity studies of peptides 23-30 toward p60c-src, Lyn, and Lck PTK showed in general high Lyn/Src and moderate Lck/Src selectivity ratios. We found that the chi1 space constraints of the specialized amino acids, introduced at position 3 of the peptide lead 23, were not as important as the configuration of the Calpha of that residue to recognize the subtle chemical environment surrounding the active site of Src and Lck PTK, as reflected on the obtained Lck/Src selectivity ratios.

Application of "one-bead one-compound" combinatorial library methods in signal transduction research

Using a "split-synthesis" solid phase synthetic approach, bead libraries can be generated such that each bead displays only one chemical entity. This "one-bead one-compound" combinatorial library can then be assayed for specific biological properties using either a solid-phase on-bead binding or functional assay, or a releasable solution phase assay. Positive compound-beads can then be isolated for structure determination. Various assay systems to screen such a "one-bead one-compound" library are described. We have used this combinatorial library method to discover peptides that bind to the cell surface immunoglobulins of murine lymphoma cells. Such peptides, when presented in an oligomeric form to a lymphoma cell are able to induce signal transduction. Additionally, we have also applied the "one-bead one-compound" combinatory library approach to elucidate peptide substrate motifs for protein tyrosine kinases. Multiple distinct peptide motifs were identified for p60(c-src) protein tyrosine kinase. Using the identified peptide substrates as templates, potent and highly specific pseudosubstrate-based peptide inhibitors were developed.

Idiotype specific peptides bind to the surface immunoglobulins of two murine B-cell lymphoma lines, inducing signal transduction

Using a random combinatorial synthetic peptide library method based on a one-bead one-peptide concept for ligand identification (Lam et. al, Nature 1991, 354, 82-84.), idiotype specific peptides were retrieved and optimized for interaction with the cell surface immunoglobulins [IgM(kappa)] of two murine B lymphoma cell lines. Several of the identified peptides were characterized with respect to cell binding and signal transduction. These peptides were able to bind specifically to the surface immunoglobulins of these lymphoma cells. In addition to binding, when synthesized in tetrameric or multimeric forms, the peptides were able to trigger signal transduction resulting in an increase in protein tyrosine phosphorylation. Since D-amino acid peptide libraries were used in some of our efforts to identify binding ligands, several of the idiotype-specific peptides are composed of all D-amino acids (e.g. wGeyvmvnG). These findings may have important therapeutic implications for targeted-therapy of B-cell lymphoma as these D-amino acid ligands are more resistant to proteolysis resulting in a prolonged pharmacokinetic disposition in vivo.

Potent pseudosubstrate-based peptide inhibitors for p60(c-src) protein tyrosine kinase

We recently reported the identification of GIYWHHY as an efficient and specific substrate for p60(c-src) protein tyrosine kinase (PTK) by screening a secondary random peptide library (Q. Lou et al., Bioorg. Med. Chem., 4: 677-682, 1996). Based on the primary structure of GIYWHHY, we designed and synthesized several pseudosubstrate-based peptide inhibitors. Some of these peptide inhibitors are highly potent and specific with IC50 in the low micromolar range. Because both YIYGSFK and GIYWHHY are efficient and specific substrates for p60(c-src) PTK, chimeric branched peptides based on these two sequences were synthesized. These branched peptides inhibit p60(c-src) PTK with high potency, indicating that the enzyme-active site of p60(c-src) PTK can accommodate more than a linear motif. This may explain why seemingly several peptides with very different linear structures can all be phosphorylated by this enzyme.

Rapid and effective method for preparation of fecal specimens for PCR assays

We have developed a novel method for the preparation of fecal specimens for PCR assays. Approximately 100 mg of solid stool or 200 microliters of liquid fecal sample was thoroughly suspended in 1 ml of water. Fecal debris was removed by low-speed centrifugation (2,800 x g for 2 min). The supernatant was then boiled for 10 min in a water bath and further clarified by high-speed centrifugation (12,000 x g for 5 min). Fifty microliters of the clarified supernatant was then purified by Sepharose CL-6B spin column chromatography, and a portion of the purified supernatant was used for PCR. By this method, stools containing enterotoxigenic Escherichia coli H10407 were amplified by colonization factor antigen I fimbrial gene PCR, with a sensitivity of 100 organisms per reaction. The method was also effective for processing stool specimens for Clostridium difficile toxin A and B gene PCRs. This method is rapid, effective, and simple to perform and will improve the applications of PCR to stool specimens for diagnostic purposes.

Evaluation of 16S rRNA gene PCR with primers Hp1 and Hp2 for detection of Helicobacter pylori

The PCR primer set Hp1-Hp2, which amplifies a 109-bp fragment of the 16S rRNA gene of Helicobacter pylori, has been widely used for the detection of H. pylori in clinical specimens. We have examined 34 stool samples and 50 human tissue samples from H. pylori-infected and uninfected patients, five human leukocyte samples, and one human cell line by this PCR method. All of these specimens produced a 109-bp PCR product. When Escherichia coli DNA was used as the template, several nonspecific bands, but not the 109-bp band, were observed. No PCR products were generated when DNA samples from five different fungi were used as templates. These results indicate that this 109-bp PCR product was amplified from the human genome. The 109-bp PCR product generated from various clinical specimens also hybridized with the probe pHp, corresponding to a region internal to the PCR product of Hp1-Hp2. We conclude that the 16S rRNA gene PCR with the primer set Hp1-Hp2 is not specific and cannot be used to detect H. pylori in clinical specimens.

Identification of GIYWHHY as a novel peptide substrate for human p60c-src protein tyrosine kinase

We have recently determined that -Ile-Tyr- were the two critical residues as a peptide substrate for p60c-src protein tyrosine kinase (Lou, Q. et al., Lett. Peptide Sci., 1995, 2, 289). Here, we report on the design and synthesis of a secondary 'one-bead, one-compound' combinatorial peptide library based on this dipeptide motif (XIYXXXX, where X = all 19 eukaryotic amino acids except for cysteine). This secondary library was screened for its ability to be phosphorylated by p60c-src PTK using [gamma 32P]ATP as a tracer. Five of the strongest [32P]-labeled peptide-beads were identified and microsequenced: GIYWHHY, KIYDDYE, EIYEENG, EIYEEYE, and YIYEEED. A solid-phase phosphorylation assay was used to evaluate the structure-activity relationship of GIYWHHY. It was determined that Ile2, Tyr3, His5, and His6 were crucial for its activity as a substrate.

Helicobacter pylori infection in recurrent abdominal pain in childhood: comparison of diagnostic tests and therapy

OBJECTIVE

To determine the role of Helicobacter pylori infection in children with recurrent abdominal pain and the usefulness of serologic tests in screening H pylori infection and monitoring treatment of H pylori-associated gastritis.

METHODS

During a 3 year period, we investigated the presence of serum immunoglobulin G (IgG) antibody to H pylori in 456 children using the high-molecular-weight cell-associated protein H pylori enzyme immunoassay kit. Among the 456 children studied, 218 (age range, 3 to 18 years; mean age, 9.5 years) had symptoms of recurrent abdominal pain (RAP syndrome) with or without vomiting, and the remaining 238 (age range, 3 to 18 years; mean age, 9.8 years) had no RAP (non-RAP syndrome). We performed upper gastrointestinal endoscopy on 111 consecutive children of the 218 with RAP syndrome and obtained mucosal biopsies for culture, histologic analysis, CLO test (Delta West, Perth, Australia), and H pylori detection by polymerase chain reaction.

RESULTS

Thirty-eight (17.4%) of 218 children in the RAP group and 25 (10.5%) of 238 children in the non-RAP group were seropositive for H pylori. Of the 111 children endoscoped, 95 were found to be negative, and 12 were positive by all five assays. Specimens from 2 children were negative by culture and the CLO test but positive by the other three assays. Specimens from 1 child were negative by histologic analysis but positive by all other tests. The remaining child was positive for anti-H pylori IgG but negative by all of the other four assays. Upper gastrointestinal endoscopy detected 14 children with peptic ulcer disease (9 duodenal ulcer and 5 gastric ulcer) and 12 with antral nodular gastritis. Only 4 of the 14 diagnosed with peptic ulcer were H pylori positive by all five assays, whereas all 12 children with antral nodular gastritis were H pylori positive. Nine of the 12 H pylori-positive children were treated with a combination of bismuth subsalicylate, amoxicillin, and metronidazole for 2 weeks. Sera obtained at 2, 4, and 6 months after treatment from all 9 children showed a decrease in anti-H pylori IgG titer. Three H pylori-infected children who did not receive any treatment served as control children, and their IgG levels remained elevated or increased over time.

CONCLUSION

The results from our study indicate that screening for the serum IgG antibody to H pylori is a practical method for diagnosing H pylori infection in children, and that serial measurements of the H pylori IgG antibody are useful for monitoring treatment of H pylori because of its high sensitivity and ease of performance. Only 4 of the 14 children diagnosed with peptic ulcer disease were confirmed to be infected with H pylori, whereas all 12 children with antral nodular gastritis were found to be infected by H pylori. These observations suggest that H pylori infection is more frequently associated with gastritis than with peptic ulcer disease in children, and that H pylori gastritis is a cause of RAP syndrome in children.

Identification and characterization of a novel synthetic peptide substrate specific for Src-family protein tyrosine kinases

Using a random combinatorial peptide library method [Wu, J., Ma, Q. N. & Lam, K. S. (1994) Biochemistry 33, 14825-14833] a novel peptide, YIYGSFK, was identified as a substrate for p60c-src protein tyrosine kinase. Mass spectrometric analysis showed that tyrosine-3 from the N-terminus was the phosphorylation site. Kinetic studies showed that the Km of YIYGSFK for p60c-src was 55 microM, about 6.4-fold lower than a peptide derived from p34cdc2 [cdc2(6-20), KVEKIGEGTYGVVYK], which had been reported to be a specific and efficient substrate for the Src-family protein tyrosine kinases. Comparison of the specificity of YIYGSFK and cdc2(6-20) as a substrate for various Src-family and non-Src-family protein tyrosine kinases suggests that YIYGSFK is a much more specific and efficient substrate for the Src-family protein tyrosine kinases.

Operation of a Ti:sapphire laser pumped by a 499-nm green laser

We report, for the first time, to our knowledge, the operation of a tunable Ti:sapphire laser pumped by a third-order Raman XeCl-H(2) laser system at 499 nm with a 60-ns pulse duration. The slope efficiency is 59% for this laser, producing pulses of 20-ns duration. The highest conversion-energy efficiency obtained is 41%, with an output energy of 1.2 mJ. The tuning range for a single set of cavity mirrors is 680-834 nm and is limited mainly by the mirror reflectivity. This study shows that a combined laser system based on a XeCl excimer laser can offer wavelength diversity.