Preoperative prediction and histological stratification of intracranial solitary fibrous tumours by machine-learning models

AIM

To explore the effectiveness and feasibility of machine-learning models based on magnetic resonance imaging (MRI) radiomics features in differentiating intracranial solitary fibrous tumour (ISFT) from angiomatous meningioma (AM) and stratifying ISFT histologically.

MATERIALS AND METHODS

This study retrospectively recruited 268 patients with a histological diagnosis of ISFT (n=120) or AM (n=148), and 116 of the ISFT patients were used for stratified analysis of histological grade. The radiomics features were extracted from axial T1-weighted imaging (WI), T2WI and contrast-enhanced T1WI sequences. All patients were assigned randomly to the training group and test group in a ratio of 7:3. The models were optimised by 10-fold cross-validation in the training group, and the independent test group was used for further testing of the models. The performances of machine-learning models based on radiomics, clinical, and fusion features in predicting and stratifying ISFT were evaluated.

RESULTS

ISFT and AM differed significantly in terms of age, tumour shape, enhancement pattern, and margin. There was no significant difference in the clinical characteristics between World Health Organization (WHO) grade II and WHO grade III ISFT. When used to differentiate ISFT from AM, the area under the curve (AUC) values of the machine-learning models based on radiomics, clinical, and fusion features in the test group were 0.917, 0.923 and 0.950, respectively. When used for histological stratification of ISFT, the model based on the radiomics signature achieved an AUC value of 0.786 in the test group.

CONCLUSIONS

Machine-learning models can contribute in the prediction and histological stratification of ISFT non-invasively, which can help clinical differential diagnosis and treatment decisions.

Bone density in youth with prediabetes: results from the National Health and Nutrition Examination Survey, 2005-2006

Youth with type 2 diabetes might have suboptimal peak bone mass, but it is unknown whether similar effects are evident in youth with prediabetes. Results from this study suggest that diabetes-related effects on peak bone mass likely occur before disease onset, and involve the muscle-bone unit.

INTRODUCTION

Type 2 diabetes might adversely influence bone health around the age of peak bone mass, but it is unknown whether diabetes-related effects on areal bone mineral density (aBMD) are evident in youth with prediabetes. We compared age-related trends in aBMD and associations between lean body mass (LBM) and aBMD between children and adolescents with prediabetes vs. normal glucose regulation.

METHODS

Cross-sectional analysis of data from the National Health and Nutrition Examination Survey (2005-2006) in youth ages 12-20 years (49% female, 34% black) with prediabetes (n = 267) and normal glucose regulation (n = 1664). Whole body aBMD and LBM were assessed via DXA. LBM index (LBMI) and Z-scores for aBMD and LBMI were computed.

RESULTS

Unadjusted between-group comparisons revealed greater mean weight and LBMI Z-scores in youth with prediabetes vs. normal glucose regulation, but similar bone Z-scores between the two groups. While accounting for differences in BMI Z-score, there was a significant interaction between prediabetes status and age with respect to whole body aBMD Z-score (P < 0.05), such that children with prediabetes tended to have increased aBMD but adolescents and young adults with prediabetes tended have lower aBMD. Furthermore, the positive association between LBMI and whole body aBMD was moderated in youth with prediabetes (P < 0.001), who had slightly lower whole body aBMD for a given LBMI (P = 0.068). Lumbar spine bone measures did not differ between the two groups.

CONCLUSIONS

Type 2 diabetes-related threats to peak bone mass might occur prior to disease onset, therefore potentially impacting a considerable proportion of US youth.

The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation

The infraorder Brachyura (true or short-tailed crabs) represents a successful group of marine invertebrates yet with limited genomic resources. Here we report a chromosome-anchored reference genome and transcriptomes of the Chinese mitten crab Eriocheir sinensis, a catadromous crab and invasive species with wide environmental tolerance, strong osmoregulatory capacity and high fertility. We show the expansion of specific gene families in the crab, including F-ATPase, which enhances our knowledge on the adaptive plasticity of this successful invasive species. Our analysis of spatio-temporal transcriptomes and the genome of E. sinensis and other decapods shows that brachyurization development is associated with down-regulation of Hox genes at the megalopa stage when tail shortening occurs. A better understanding of the molecular mechanism regulating sexual development is achieved by integrated analysis of multiple omics. These genomic resources significantly expand the gene repertoire of Brachyura, and provide insights into the biology of this group, and Crustacea in general.

miR-199a impairs autophagy and induces cardiac hypertrophy through mTOR activation

Basal autophagy is tightly regulated by transcriptional and epigenetic factors to maintain cellular homeostasis. Dysregulation of cardiac autophagy is associated with heart diseases, including cardiac hypertrophy, but the mechanism governing cardiac autophagy is rarely identified. To analyze the in vivo function of miR-199a in cardiac autophagy and cardiac hypertrophy, we generated cardiac-specific miR-199a transgenic mice and showed that overexpression of miR-199a was sufficient to inhibit cardiomyocyte autophagy and induce cardiac hypertrophy in vivo. miR-199a impaired cardiomyocyte autophagy in a cell-autonomous manner by targeting glycogen synthase kinase 3β (GSK3β)/mammalian target of rapamycin (mTOR) complex signaling. Overexpression of autophagy related gene 5 (Atg5) attenuated the hypertrophic effects of miR-199a overexpression on cardiomyocytes, and activation of autophagy using rapamycin was sufficient to restore cardiac autophagy and decrease cardiac hypertrophy in miR-199a transgenic mice. These results reveal a novel role of miR-199a as a key regulator of cardiac autophagy, suggesting that targeting miRNAs controlling autophagy as a potential therapeutic strategy for cardiac disease.

A heterozygous moth genome provides insights into herbivory and detoxification

How an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants, but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood. We report the first whole-genome sequence of a basal lepidopteran species, Plutella xylostella, which contains 18,071 protein-coding and 1,412 unique genes with an expansion of gene families associated with perception and the detoxification of plant defense compounds. A recent expansion of retrotransposons near detoxification-related genes and a wider system used in the metabolism of plant defense compounds are shown to also be involved in the development of insecticide resistance. This work shows the genetic and molecular bases for the evolutionary success of this worldwide herbivore and offers wider insights into insect adaptation to plant feeding, as well as opening avenues for more sustainable pest management.

The genome of the pear (Pyrus bretschneideri Rehd.)

The draft genome of the pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 194× coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these, ∼28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other ∼5.4–21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30–45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C3′H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.

Measurement of Aflatoxin and Aflatoxin Metabolites in Urine by Liquid Chromatography-Tandem Mass Spectrometry

Automated immunoaffinity solid-phase extraction followed by liquid chromatography-tandem mass spectrometry and chemical analogue internal standardization is employed to detect and quantify the aflatoxins AFB(1), AFB(2), AFG(1), AFG(2), and the metabolites AFM(1) and AFP(1) in urine. The dynamic range of the method is nearly three orders of magnitude with limits of detection in the low femtogram on column range. The method was validated over a 12-day period by eight analysts. This method is suitable for agricultural, forensic, and public health laboratories during an accidental outbreak or a chemical terrorism event where a rapid and accurate diagnosis of aflatoxicosis is needed.

[Comprehensive utilization and development of traditional Tibetan medicine in China]

OBJECTIVE

To deal with the further investigation field by discussing the status and present problem of traditional Tibetan medicine.

METHOD

Previous relevant investigations and literatures were summed up in the field. The present situation of traditional Tibetan medicine in China was analysed.

RESULT

The textual research, basic medicinal property, exploration of developable medicinal resource and protection of endangered medicinal species etc. were elaborated and the key problem of further investigation in 21st century was expounded.

CONCLUSION

The textual research, basic medicinal property, exploration of develoable medicinal resources, especially monographic study on protection of major endangered medicinal resources should be intensified. Domestication and cultivation, and exploration of good-quality medicinal resources, quality evaluation and exploitation of effectual prescriptions are the focal field in the study of traditional Tibetan medicine.

L-Altruronic acid formed by epimerization of D-galacturonic acid methyl esters during saponification of citrus pectin

While searching for oligosaccharides containing rhamnose residues in the endopolygalacturonase (EPG) digest of saponified citrus pectin, we found several oligomers containing, in addition to galacturonic acid, a sugar previously unreported in pectin. The 1- and 2-D 1H NMR spectra of the oligosaccharides were consistent with the sugar being a uronic acid with its 2- and 3-hydroxyls being axial and 4-hydroxyl being equatorial. MALDI-TOF mass spectrometry indicated that the oligomers consisted solely of uronic acids. Reduction of the uronic acids in the oligosaccharides converted them to galactose and altrose. The altrose was found to be the L enantiomer by comparison of its trimethylsilyl (-)-2-butyl glycosides to those of authentic D-altrose and a racemic mixture. The sugar was not found in oligosaccharides prepared from EPG digestion of citrus pectin deesterified with pectin methylesterase rather than saponification. Thus, it appears that during saponification, a small proportion of the methylesterified galacturonic acid residues in pectins is epimerized at C-5 leading to formation of L-altruronic acid residues.

Binding of the human papillomavirus type 16 E7 oncoprotein and the adeno-associated virus Rep78 major regulatory protein in vitro and in yeast and the potential for downstream effects

OBJECTIVE

Both human papillomavirus (HPV) and adeno-associated virus (AAV) are common anogenital viruses and likely co-infect the epithelium in vivo. However, whereas HPVs are positively associated with cervical cancer, AAV appears to be negatively associated. In tissue culture, AAV-encoded Rep78--which is essential for AAV--inhibits gene expression and oncogenic transformation by HPV-16/18 and bovine papillomavirus type 1. Here we observed whether the HPV-16 E7 oncoprotein might recognize and bind Rep78. Further, upon finding Rep78-E7 binding, we investigated some of the potential downstream effects such an interaction might have. E7 is capable of recognizing a variety of proteins, including RB105, TATA box-binding protein (TBP), TBP-associated factor (TAF)(II)110, E2F, cyclins A and D, and c-jun. Some of these interactions are likely responsible for E7's cancer-promoting activity.

STUDY DESIGN/METHODS

Rep78-E7 interaction was investigated in vitro by West(far)-Western and affinity chromatography analysis and in vivo in living yeast by the GAL4 two-hybrid cDNA assay. Mapping of the E7 binding domain within Rep78 was carried out using a series of amino- and carboxy-truncated Rep78 proteins in a West(far)-Western assay. Downstream effects of the interaction were analyzed by competitive affinity chromatography (protein-protein) and competitive electrophoretic mobility shift assay (protein-DNA).

RESULTS

E7 and Rep78 were found to interact both in vitro and in vivo (yeast) in all assays attempted. The E7 binding domain within Rep78 was found to reside within amino acids 121-370. Regarding downstream effects of this interaction, Rep78 was found to mildly inhibit E7-TAF(II)110 and E7-RB105 interaction in vitro but to have little affect on E7-TBP interaction. Finally, it was found that E7 was able to affect Rep78's interaction with AAV's terminal repeat (TR) DNA in vitro, reducing the formation of the largest sized Rep78-TR complexes in a dosage-dependent manner.

CONCLUSIONS

These data suggest that the Rep78-E7 interaction may have repercussions for both viruses. The Rep78-E7 interaction may be a second mechanism, in addition to Rep78 regulation of the p97 promoter, by which AAV inhibits HPV-16 oncogenic transformation. These data also suggest that HPV-16 may affect the AAV life cycle by altering Rep78-TR interaction.

Binding of the human papillomavirus type 16 p97 promoter by the adeno-associated virus Rep78 major regulatory protein correlates with inhibition

Human papillomavirus type 16 (HPV-16) infection is positively associated with cervical cancer, whereas adeno-associated virus (AAV) infection is negatively associated with this same cancer. In earlier studies these two virus types have been shown to directly interact, with AAV inhibiting or enhancing papillomavirus functions depending upon the specific circumstances. One defined interaction between these two viruses is the ability of the AAV Rep78 major regulatory protein to inhibit gene expression of the E6 promoter of BPV-1 (bovine papillomavirus type 1) and HPV types 16 and 18. As Rep78 is a DNA binding transcription factor, we considered whether Rep78 might bind HPV-16 DNA. Here, Rep78 is demonstrated to bind a 44-base pair region (nucleotides 14-56) within the HPV-16 p97 promoter using the electrophoretic mobility shift assay. This region is important for HPV-16 because it includes functional Sp1 and E2 protein binding motifs as well as part of the origin of replication. Furthermore, two Rep78 amino acid substitution mutants, at positions 77 or 64-65, were identified that did not recognize p97 DNA. Both of these Rep78 mutants were found to be defective for inhibition of p97 promoter activity in HeLa and T-47D nuclear extracts in vitro, in a transient chloramphenicol acetyltransferase assay, as well as defective for full inhibition of HPV-16-directed focus formation. These data, taken together, strongly suggest that the Rep78-p97 promoter interaction is at least partially responsible for Rep78-mediated inhibition of HPV-16. Finally, the finding that Rep78 specifically recognizes p97 DNA is surprising because the p97 promoter region contains no GAGC motifs, the core motif for Rep78 recognition. These data suggest that the p97 promoter may represent a new prototypical DNA target type for Rep78.

Induction of human papillomavirus-specific CD4(+) and CD8(+) lymphocytes by E7-pulsed autologous dendritic cells in patients with human papillomavirus type 16- and 18-positive cervical cancer

Human papillomavirus (HPV) type 16 (HPV 16) and HPV type 18 (HPV 18) are implicated in the induction and progression of the majority of cervical cancers. Since the E6 and E7 oncoproteins of these viruses are expressed in these lesions, such proteins might be potential tumor-specific targets for immunotherapy. In this report, we demonstrate that recombinant, full-length E7-pulsed autologous dendritic cells (DC) can elicit a specific CD8(+) cytotoxic T-lymphocyte (CTL) response against autologous tumor target cells in three patients with HPV 16- or HPV 18-positive cervical cancer. E7-specific CTL populations expressed strong cytolytic activity against autologous tumor cells, did not lyse autologous concanavalin A-treated lymphoblasts or autologous Epstein-Barr virus-transformed lymphoblastoid cell lines (LCL), and showed low levels of cytotoxicity against natural killer cell-sensitive K562 cells. Cytotoxicity against autologous tumor cells could be significantly blocked by anti-HLA class I (W6/32) and anti-CD11a/LFA-1 antibodies. Phenotypically, all CTL populations were CD3(+)/CD8(+), with variable levels of CD56 expression. CTL induced by E7-pulsed DC were also highly cytotoxic against an allogeneic HLA-A2(+) HPV 16-positive matched cell line (CaSki). In addition, we show that specific lymphoproliferative responses by autologous CD4(+) T cells can also be induced by E7-pulsed autologus DC. E7-specific CD4(+) T cells proliferated in response to E7-pulsed LCL but not unpulsed LCL, and this response could be blocked by anti-HLA class II antibody. Finally, with two-color flow cytometric analysis of intracellular cytokine expression at the single-cell level, a marked Th1-like bias (as determined by the frequency of gamma interferon- and interleukin 4-expressing cells) was observable for both CD8(+) and CD4(+) E7-specific lymphocyte populations. Taken together, these data demonstrate that full-length E7-pulsed DC can induce both E7-specific CD4(+) T-cell proliferative responses and strong CD8(+) CTL responses capable of lysing autologous naturally HPV-infected cancer cells in patients with cervical cancer. These results may have important implications for the treatment of cervical cancer patients with active or adoptive immunotherapy.

Use of scavenger beads to remove excess labeling reagents from capillary zone electrophoresis samples

In many cases, samples for capillary zone electrophoresis (CZE) are derivatized with a chromophore or fluorophore to enhance their detectability. To ensure efficient labeling, a large excess of labeling agent is often used, which leads to the presence of a large peak for unreacted reagent. Here we report that excess reagent can be reacted with "scavenger beads" carrying an appropriate functional group to remove it from the sample solution. We present examples of removal of aminonaphthalene mono-, di-, and trisulfonic acid from mixtures in which they were used to label mono- or oligosaccharides by reductive amination. Aldehyde-containing scavenger beads were made by oxidizing Sephadex G-50 beads with sodium periodate. These were added to the labeling reaction mixtures after the reductive amination of the sugars was complete. Almost complete elimination of the peak from the labeling agent could be achieved.

Scarcity or complete lack of single rhamnose residues interspersed within the homogalacturonan regions of citrus pectin

Commercial citrus pectin containing galacturonic acid and rhamnose in a ratio of approximately 40:1 was saponified and then exhaustively digested with endopolygalacturonase (EPG). The products were separated by ultrafiltration into low-molecular-weight (LMW) and high-molecular-weight (HMW) fractions. The LMW fraction accounted for 80% of the starting material, but for only 10% of the total rhamnose. The molar ratio of galacturonic acid to rhamnose of the LMW fraction was 236, suggesting that very few small Rha-containing oligomers were generated by the EPG digestion. No distinct Rha-containing oligomers were found by various chromatographic analyses of the LMW fraction. The HMW fraction, which only accounted for 10% by weight of the starting pectin, contained more than 85% of the rhamnose. The ratio of GalA to Rha in the HMW fraction was 1.7:1 and partial acid hydrolysis of this fraction produced a series of oligomers consisting of GalA-Rha repeating units, suggesting that it contained rhamnogalacturonan, which has a backbone composed of GalA-Rha disaccharide repeating units. The HMW fraction also contained large amounts of arabinose and galactose, which probably originated from side chains linked to some of the rhamnose residues. We propose that commercial citrus pectin is composed of two regions: the predominant region consists of chains of uninterrupted 1,4-linked alpha-D-GalA residues with between 60-70% of the residues methyl esterified; and the other region consists of rhamnogalacturonan with a backbone composed of GalA-Rha disaccharide repeating units and neutral sugar side chains.

The adeno-associated virus Rep78 major regulatory protein binds the cellular TATA-binding protein in vitro and in vivo

Rep78 is the major regulatory protein of adenoassociated virus (AAV). Rep78 is able to transcriptionally regulate all three of AAV's promoters, as well as a variety of heterologous promoters. In an attempt to understand the mechanism of action by which Rep78 is able to regulate gene expression, we are investigating Rep78's possible protein-protein interaction with basal transcription factors. One such critical basal transcription factor is the human TATA binding protein, TBP. TBP is a core factor required for the assemblage of the transcription initiation complex, TFIID. In this report an in vitro interaction between Rep78 and TBP was demonstrated in three different assay systems, including West(far)-Western analysis, electrophoretic mobility shift assay-supershift, and coimmunoprecipitation. Furthermore, using the yeast GAL4 two-hybrid system, an in vivo interaction between Rep78 and TBP was also demonstrated. Further still, the amino half of Rep78 is shown to be needed for Rep78-TBP interaction. Mutations within this region of Rep78 are known to be defective for transcriptional regulatory ability, suggesting a biological role for this interaction. Thus, Rep78 may regulate transcription through binding and regulating TBP's numerous interactions. Furthermore, as Rep78 is known to bind at least one other transcription factor (Sp 1) and likely others, Rep78 may function as a TBP-associated factor in an altered TFIID-like complex.

Synthesis and 32P-postlabeling/high-performance liquid chromatography separation of diastereomeric 1,N2-(1,3-propano)-2'-deoxyguanosine 3'-phosphate adducts formed from 4-hydroxy-2-nonenal

4-Hydroxy-2-nonenal (HNE), a major electrophilic byproduct of lipid peroxidation, is mutagenic and cytotoxic. The two pairs of HNE-derived diastereomeric 1,N2-propanodeoxyguanosine 3'-monophosphate adducts were synthesized from reaction of HNE with 2'-deoxyguanosine 3'-monophosphate. After HPLC separation, these adducts were characterized by UV-visible absorption and negative ion electrospray ionization MS/MS analysis. To further characterize the structures, these adducts were dephosphorylated to the corresponding HNE-modified deoxyguanosine adducts and their HPLC retention times and UV spectra were compared with those of the synthetic standards prepared from reaction of HNE with 2'-deoxyguanosine. Separation of these adducts by 32P-postlabeling/HPLC was developed. Reaction of HNE with calf thymus DNA resulted in only one pair of diastereomeric adducts, with one adduct predominantly formed with a modification level of 1.2 +/- 0.5 adducts/10(7) nucleotides.