Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine

A grand challenge impeding optimal treatment outcomes for patients with cancer arises from the complex nature of the disease: the cellular heterogeneity, the myriad of dysfunctional molecular and genetic networks as results of genetic (somatic) and environmental perturbations. Systems biology, with its holistic approach to understanding fundamental principles in biology, and the empowering technologies in genomics, proteomics, single-cell analysis, microfluidics and computational strategies, enables a comprehensive approach to medicine, which strives to unveil the pathogenic mechanisms of diseases, identify disease biomarkers and begin thinking about new strategies for drug target discovery. The integration of multidimensional high-throughput 'omics' measurements from tumour tissues and corresponding blood specimens, together with new systems strategies for diagnostics, enables the identification of cancer biomarkers that will enable presymptomatic diagnosis, stratification of disease, assessment of disease progression, evaluation of patient response to therapy and the identification of reoccurrences. Whilst some aspects of systems medicine are being adopted in clinical oncology practice through companion molecular diagnostics for personalized therapy, the mounting influx of global quantitative data from both wellness and diseases is shaping up a transformational paradigm in medicine we termed 'predictive', 'preventive', 'personalized', and 'participatory' (P4) medicine, which requires new strategies, both scientific and organizational, to enable bringing this revolution in medicine to patients and to the healthcare system. P4 medicine will have a profound impact on society - transforming the healthcare system, turning around the ever escalating costs of healthcare, digitizing the practice of medicine and creating enormous economic opportunities for those organizations and nations that embrace this revolution.

Are bone mineral density loci associated with hip osteoporotic fractures? A validation study on previously reported genome-wide association loci in a Chinese population

Osteoporosis is a heritable disease characterized mainly by low bone mineral density (BMD) and/or osteoporotic fractures (OF). Most genome-wide association studies on osteoporosis have focused on BMD, whereas little effort has been expended to identify genetic variants directly linked to OF. To determine whether BMD-loci are also associated with OF risk, we performed a validation study to examine 23 BMD-loci reported by recent genome-wide association studies for association with hip OF risk. Our sample consisted of 700 elderly Chinese Han subjects, 350 with hip OF and 350 healthy matched controls. We identified four BMD-loci that were significantly associated with hip OF in this Chinese population, including 7q21 (FLJ42280, P = 1.17 × 10(-4) for rs4729260; P = 0.008 for rs7781370), 6p21 (MHC, P = 0.004 for rs3130340), 13q14 (TNFSF11, P = 0.012 for rs9533090; P = 0.018 for rs9594759; P = 0.020 for rs9594738; P = 0.044 for rs9594751), and 18q21 (TNFRSF11A, P = 0.015 for rs884205). The SNP rs4729260 at 7q21 remained significantly associated, even after conservative Bonferroni's correction. Our results further highlight the importance of these loci in the pathogenesis of osteoporosis, and demonstrate that it is feasible and useful to use OF as the direct phenotype to conduct genetic studies, to enhance our understanding of the genetic architecture of osteoporosis.

Genetic variation and clonal diversity of Bromus ircutensis Kom. in the Otingdag sandy land detected by ISSR markers

Genetic variation and clonal diversity of nine populations of Bromus ircutensis Kom. from the Otingdag sandy land were investigated using Inter Simple Sequence Repeat (ISSR) markers. A total of 102 bands were amplified by using II ISSR primers chosen for the study. Among those 99% were polymorphic indicating high level of genetic variation at the species level with a mean genetic diversity (H) of 0.292 and Shannon information index (1) of 0.450. Percentage of polymorphic loci (PPL) of nine populations was 76.48% on average, which provides more evidence of considerable genetic variation at the population level. AMOVA analysis revealed that total genetic variation was higher within populations (87.06%) than between populations (12.94%), which is mainly the result of the extensive gene flow (Nm = 1.682) among B. ircutensis populations. UPGMA cluster analysis divided the nine populations into two groups. There was significant or moderate negative correlations between genetic diversity parameters (PPL, H, 1) and longitude or latitude. Mantel test also showed a significant correlation between geographical distance and genetic distance (r = 0.681, p = 0.002). Our findings indicated that distribution of B. ircutensis populations was influenced by geographical and ecological factors. Clonal diversity was also high with 108 individuals identified by 11 ISSR primers being all of different genets. Our results provide a molecular basis for sustainable management and conservation ofB. ircutensis in the study area.

Phenylbutyric acid prevents rats from electroconvulsion-induced memory deficit with alterations of memory-related proteins and tau hyperphosphorylation

Electroconvulsive therapy has been commonly applied in the treatment of refractory depression, but its cognitive side effects are noticed and restrict its application. The molecular mechanisms underlying the side effects remain elusive, and there is no efficient prevention. By employing a recognized electroconvulsive shock (ECS) rat model, we found in the present study that ECS induced spatial memory deficits with simultaneous decreases in synaptic proteins of N-methyl-D-aspartate receptor 2A/B (NR2A/B) and postsynaptic density 95 (PSD95), the immediate early gene c-Fos and cAMP response element binding (CREB) proteins, all of which are memory-related proteins. ECS also caused tau hyperphosphorylation at multiple Alzheimer-related phosphorylation sites with activation of glycogen synthase kinase-3beta (GSK-3beta), Akt and phospho-PKR-like endoreticulum (PERK), and inhibition of protein phosphatase-2A (PP)-2A. Intraperitoneal injection of phenylbutyric acid (PBA), an aromatic short chain fatty acid with the functions of molecule chaperon, prevented rats from the ECS-induced memory deficits, alterations of the memory-associated proteins, and tau hyperphosphorylation. Our data suggest that PBA may be potentially used for attenuating the side effects caused by electroconvulsive therapy.

The nonsynonymous single-nucleotide polymorphisms in codon 31 of p21 gene and the susceptibility to cervical cancer in Chinese women

BACKGROUND

It was suggested that single-nucleotide polymorphisms in p21 codon 31 seem to be associated with a variety of human malignancies; very few studies have focused on the association between p21 codon 31 polymorphisms and cervical cancer. This study explored whether p21 codon 31 nonsynonymous single-nucleotide polymorphisms might be associated with an increased risk of cervical cancer development among Chinese women.

METHODS

Peripheral blood samples were obtained from patients with cervical cancer (n = 317) and healthy controls (n = 353) for detecting the biallelic polymorphisms at codon 31 of p21 gene by the mismatch amplification mutation assay-polymerase chain reaction. Cervix brush-off samples were obtained from patients with cervical squamous cell carcinoma (SCC) and controls for detection of high-risk human papillomavirus (HR-HPV).

RESULTS

The AGA (Arg) allele frequency in patients with cervical SCCs was significantly higher than that in controls. AGA/AGA and AGA/AGC genotypes were more frequently found in cervical SCCs than in controls. There was no significant difference of allele frequency or genotype distribution between cervical adenocarcinomas and controls, or between HR-HPV-positive and HR-HPV-negative groups.

CONCLUSIONS

p21 Codon 31 with AGA (Arg) allele is a genetic risk factor of cervical SCC, and the increased risk is probably not caused by increasing host susceptibility to HR-HPV infection.

Regulation of expression of cd133, a colon cancer stem cell marker and other stemness genes/pathways, by celecoxib: Clues from clinical observations

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Background: CD133 identifies intestinal stem cells and colon CSC, the putative culprit of cancer initiation, progression and resistance. Elevated CD133 levels at protein & mRNA levels predict poor outcomes in patients (pts) with colon cancer. Given that celecoxib reduces colon polyp and only maintenance capecitabine plus celecoxib lead to paradoxically high complete remission (CR) in colon cancer pts who had no resection or positive margin resection of metastases (ASCO 2007), we hypothesized that celecoxib could modulate CD133 and other stemness genes/signaling pathways. Methods: we studied the effects of celecoxib versus 5-FU on CD133, Wnt and other stemness genes/pathways using flow cytometry, immunoflurorescence, real time RT-PCR, western blot, TOP-Flash for Wnt, limiting dilution assay, and Affymetrix in colon cancer cell lines and primary colon cancer spheres. Results: Celecoxib or 5FU inhibited the growth of COX-2+ HT29 or COX-2- DLD1 that express CD133 at 80% and 30% respectively. Only celecoxib down-regulated CD133 expression at the mRNA, and protein levels in a dose and time dependent manner. This effect could not be rescued with PGE2 and may be due to Wnt inhibition. Microarray showed 4 folds down-regulation of CD133 and other stemness genes e.g. CD24, ABC transporters, and LGR4/5, findings of colon cancer sphere under differentiation. Celecoxib affected several key stem cells signaling pathway, restored RB and promote cell cycle progression (P < 0.05). In contrast, 5FU affected G2M transition but had no effects on stemness genes/pathways (p < 0.05). Celecoxib resulted in 6–10 folds reduction in colony size and number with 5.6–36 folds down-regulation of CD133 mRNA in primary colon cancer spheres. Pts with confirmed radiographic CR who had received >6 months of maintenance capecitabine and celecoxib reached 5-year survival > 90% comparable to pts who achieved pathological CR (12/19). Conclusions: Targeting colon CSC with capecitabine and celecoxib may lead to durable CR and survival and deserves further investigation.

No significant financial relationships to disclose.

Iris recognition based on key image feature extraction

In iris recognition, feature extraction can be influenced by factors such as illumination and contrast, and thus the features extracted may be unreliable, which can cause a high rate of false results in iris pattern recognition. In order to obtain stable features, an algorithm was proposed in this paper to extract key features of a pattern from multiple images. The proposed algorithm built an iris feature template by extracting key features and performed iris identity enrolment. Simulation results showed that the selected key features have high recognition accuracy on the CASIA Iris Set, where both contrast and illumination variance exist.

Retrieving leaf area index for coniferous forest in Xingguo County, China with Landsat ETM+ images

Spatial distributions of the leaf area index (LAI) needed for carbon cycle modeling in Xingguo County, China were estimated based on correlations between the field-measurements and vegetation indices (VIs). After making geometric and atmospheric corrections to two Landsat ETM+ images, one in January 2000 and the other in May 2003, three VIs (SR, NDVI, and RSR) were derived, and their separate correlations with ground LAI measurements were established. The correlation with RSR was the highest among the three VIs. The retrieved LAI values for January 2000 were lower than those for May 2003 because of a small seasonal variation in the coniferous forests (predominantly masson pine) and the decrease in the understorey vegetation during winter.

Spatial scaling between leaf area index maps of different resolutions

We developed algorithms for spatial scaling of leaf area index (LAI) using sub-pixel information. The study area is located near Liping County, Guizhou Province, in China. Methods for LAI spatial scaling were investigated on LAI images with 960 m resolution derived in two ways. LAI from distributed calculation (LAID) was derived using Landsat ETM+ data (30 m), and LAI from lumped calculation (LAIL) was obtained from the coarse (960 m) resolution data derived through resampling the ETM+ data. We found that lumped calculations can be considerably biased compared to the distributed (ETM+) case, suggesting that global and regional LAI maps can be biased if surface heterogeneity within the mapping resolution is ignored. Based on these results, we developed algorithms for removing the biases in lumped LAI maps using sub-pixel land cover-type information, and applied these to correct one coarse resolution LAI product which greatly improved its accuracy.

Enhancing forest carbon sequestration in China: toward an integration of scientific and socio-economic perspectives

This article serves as an introduction to this special issue, "China's Forest Carbon Sequestration", representing major results of a project sponsored by the Canadian International Development Agency and the Chinese Academy of Sciences. China occupies a pivotal position globally as a principle emitter of carbon dioxide, as host to some of the world's largest reforestation efforts, and as a key player in international negotiations aimed at reducing global greenhouse gas emission. The goals of this project are to develop remote sensing approaches for quantifying forest carbon balance in China in a transparent manner, and information and tools to support land-use decisions for enhanced carbon sequestration (CS) that are science based and economically and socially viable. The project consists of three components: (i) remote sensing and carbon modeling, (ii) forest and soil assessment, and (iii) integrated assessment of the socio-economic implications of CS via forest management. Articles included in this special issue are highlights of the results of each of these components.

Fetoscopy under gas amniodistension: pressure-dependent influence of helium vs nitrous oxide on fetal goats

PURPOSE

Recently, gas amniodistension has been advocated for fetoscopic surgery to employ ergonomics similar to laparoscopy. However, neither the optimal type of gas nor its physiological influence on the fetus have been clearly outlined yet. This study investigates the impact of helium (HE) vs nitrous oxide (N2O) on fetal goats during fetoscopy.

METHODS

We insufflated either HE or N2O in 12 pregnant goats (15 fetuses; HE = 7, N2O = 8), then increased the pressures from 0, 4, 7, to 10 mm Hg in 30-minute intervals and recorded the fetal and maternal vital parameters. Finally, whole-body computed tomography to asses for intracorporeal gas was performed.

RESULTS

All fetuses survived. Mean fetal vital signs showed no significant differences between HE or N2O at specific pressure levels. In detail, HE/N2O at 0 vs 10 mm Hg caused a fetal temperature decrease (32.9 degrees C/33.2 degrees C vs 32 degrees C/32.5 degrees C), heart rate increase in the N2O group (100/102 vs 102/121 beats per minute), and no significant change in arterial pressure (45.8/48.3 vs 53.7/46.7 mm Hg). The PO2 was adequate (3.7/3.3 vs 3.7/2.9 kPa), whereas the pH remained unchanged (7.4/7.3 vs 7.3/7.3). However, fetal pCO2 was elevated in the N2O group before insufflation (5.5/7.2 vs 6.8/8.0 kPa) owing to maternal hypoventilation (maternal PCO2: 4.9/5.8 vs 5.0/5.4 kPa), correction of which was slower in the fetus than in the maternal animal. Computed tomography ruled out intracorporeal gas accumulation.

CONCLUSION

Neither HE nor N2O impose significant physiological harm for the fetus. Heating of the gas and maternal anesthesia seem essential. Considering the potential teratogenicity of N2O, however, HE could be the favorable environment for fetoscopic procedures under gas amniodistension.

Endogenous overproduction of β-amyloid induces tau hyperphosphorylation and decreases the solubility of tau in N2a cells

Although neurofibrillary tangles and senile plaques have been identified as the hallmark pathological changes in the brain of Alzheimer's disease (AD), the relationship between them is still not fully understood. In the present study, we have studied the effect of endogenously overproduced amyloid beta (A beta) on tau by using wild type amyloid precursor protein (APP) transfected (N2a/APP695), or Swedish mutant APP plus Delta 9 deleted presenilin-1 co-transfected (N2a/APPswe.Delta 9) and APP vector transfected (N2a/vector) cell lines. We measured the secreted and intracellular A beta, including A beta(1-40) and A beta(1-42), by Sandwich ELISA assay. It was shown that the levels of A beta were increased time-dependently in N2a/APP695 and N2a/APPswe.Delta 9 but not in N2a/vector upon butyric acid (BA) treatment. Compared with N2a/vector cells, tau in N2a/APP695 and N2a/APPswe.Delta 9 cells was not extracted by RIPA buffer, and the SDS-extracted tau protein was hyperphosphorylated at Tau-1 and PHF-1 epitopes upon BA treatment. Obvious accumulation of the hyperphosphorylated tau in N2a/APP695 and N2a/APPswe.Delta 9 cells was observed at 48 h after BA treatment. The total level of the extracted tau was reduced in N2a/APP695 and N2a/APPswe.Delta 9 lines compared with N2a/vector cells by Western blot, and this reduction of total tau was also detected by immunofluorescence staining. No obvious alteration of tau mRNA was observed in both N2a/APP695 and N2a/APPswe.Delta 9 cells compared with N2a/vector. This study provides direct evidence demonstrating that endogenously overproduced A beta not only induces tau hyperphosphorylation but also decreases the level and solubility of tau in N2a cell lines.

Association between Polymorphisms of Vitamin D Receptor Gene ApaI, BsmI and TaqI and Muscular Strength in Young Chinese Women

The association between the polymorphisms of vitamin D receptor gene ApaI, BsmI and TaqI and isokinetic muscular strength was examined in 109 healthy, young Chinese women.

METHODS

Genomic DNA was extracted from mouthwash samples and vitamin D receptor genotypes were determined with the established methods. The peak torque of the dominant limb in concentric and eccentric knee extensors and flexors and elbow extensors and flexors was measured using Cybex-Norm-770 isokinetic dynamometer at slow and fast velocities. The distribution frequency of vitamin D receptor gene alleles was analyzed by chi-square test. The difference in muscular strength between VDR genotype groups was analyzed using one-way ANOVA. The ApaI, BsmI and TaqI alleles and genotype frequencies appeared to be in a Hardy-Weinberg equilibrium. Subjects with the vitamin D receptor ApaI null (A allele) mutation (AA) exhibited significantly lower knee and elbow concentric or eccentric peak torque than those with aa homozygous or Aa heterozygous. The BB & Bb group showed significantly higher peak torque in concentric knee flexors than bb group. No association was found between vitamin D receptor gene TaqI and muscular strength. The data indicated that vitamin D receptor gene ApaI and BsmI polymorphisms rather than TaqI polymorphism might be associated with muscular strength.

Activation of glycogen synthase kinase-3 induces Alzheimer-like tau hyperphosphorylation in rat hippocampus slices in culture

Formation of neurofibrillary tangle from hyperphosphorylated tau is one of the hallmark lesions seen in Alzheimer's disease (AD) brain, and neuronal deregulation of glycogen synthase kinase-3 (GSK-3) activity plays key role in tau hyperphosphorylation. In the present study, the role of GSK-3 on tau phosphorylation in hippocampus slice culture was examined by incubating the slice with wortmannin (WT), an inhibitor of phosphatidylinositol 3-kinase (PI3K) and GF-109203X (GFX), an inhibitor of protein kinase C (PKC). It was found that treatment of the slices with GFX or WT separately induced tau hyperphosphorylation both at Ser396/Ser404 (PHF-1) and Ser199/Ser202 (Tau-1) sites. The phosphorylation rate of tau at PHF-1 and Tau-1 epitopes was further increased when GFX and WT were used in combination, and at this condition, AD-like tau accumulation was observed. GSK-3 activity was significantly increased with a concurrently decreased level of inactivated form of GSK-3. Lithium chloride (LiCl), a GSK-3 inhibitor, prevented tau from WT- and GFX-induced hyperphosphorylation. It suggests that GSK-3 is regulated through PI3K and PKC pathway, and activation of GSK-3 not only induces hyperphosphorylation of tau but also leads to accumulation of tau in cultured rat brain slice.

Injection of okadaic acid into the meynert nucleus basalis of rat brain induces decreased acetylcholine level and spatial memory deficit

Abnormal hyperphosphorylation of tau and cholinergic deficit occur in the early stage of Alzheimer's disease (AD) and relate to the dementia symptom. Hyperphosphorylation of tau, neurofilament (NF) and other proteins in AD brain appears to be caused by a down-regulation of protein phosphatase 2A (PP2A), but the mechanism leading to cholinergic deficit is still unknown. In this study, we selectively inhibited PP2A by injection of okadaic acid (OA) into the Meynert nucleus basalis of rats. We found that injection of OA induced hyperphosphorylation of tau and NF and decreased acetylcholine (ACh) level in the nucleus basalis of Meynert. These alterations were accompanied by spatial memory deficit in OA-injected rats. We also demonstrated that the OA-induced ACh reduction may be due to a failure of intraneuronal transport of choline acetyltransferase (ChAT) from cell body to the neuronal terminals rather than an alteration of activity of ChAT or acetylcholinesterase. This study suggests that a down-regulation of PP2A may underlie both abnormal hyperphosphorylation of cytoskeletal proteins leading to neurofibrillary degeneration and cholinergic deficiency in AD.

Differential inhibition of human cancer cell proliferation by citrus limonoids

Limonoids have been shown to inhibit the growth of estrogen receptor-negative and -positive human breast cancer cells in culture. The primary objective of this study was to test the antiproliferative activity of limonoids (obacunone 17 beta-D-glucopyranoside, nomilinic acid 17 beta-D-glucopyranoside, limonin, nomilin, and a limonoid glucoside mixture), found in high concentrations in mandarin (Citrus reticulata Blanco), against a series of human cancer cell lines. The human cancer cell lines included leukemia (HL-60), ovary (SKOV-3), cervix (HeLa), stomach (NCI-SNU-1), liver (Hep G2), and breast (MCF-7). The growth-inhibitory effects of the four limonoids and the limonoid glucoside mixture against MCF-7 cells were significant, and the antiproliferative activity of the different citrus limonoids was also dose and time dependent. No significant effects were observed on growth of the other cancer cell lines treated with the four individual limonoids at 100 micrograms/ml. At 100 micrograms/ml, the limonoid glucoside mixture demonstrated a partial inhibitory effect on SKOV-3 cancer cells. With use of flow cytometry, it was found that all the limonoid samples could induce apoptosis in MCF-7 cells at relatively high concentrations (100 micrograms/ml). Considering the high concentration needed to induce apoptosis, it is unlikely that this is the primary mechanism of action for the cytotoxic effects seen with limonoids in this study. Further work is needed in this area to establish the mechanism of action of citrus limonoids on human breast cancer cells.

[Cloning of a new cDNA: responded to all-trans retinoic acid in HL-60 cell differentiation]

In this paper a new type of cDNA fragment named as W-1 gene was first cloned and sequenced from ATRA induced HL-60 cells by using differential display PCR (DD-PCR) and DNA sequencing techniques. These differentially expressing products of the gene responding to ATRA were further confirmed by Northern blotting analysis. The results showed that the expressing level of this gene induced by ATRA (10(-6) mol.L-1) for 16 hrs was much higher than that in the control HL-60 cells, but its expression in HL-60 was reduced to an unestimable level after induction of ATRA (10(-6) mol.L-1) for 24 hrs. It suggests that ATRA may increase the expression of W-1 gene during the early stage of HL-60 cell differentiation. The exact mechanism of action is being studied further.

Synthesis of 9-alkylidene-9H-fluorenes by a novel, palladium-catalyzed cascade reaction of aryl halides and 1-aryl-1-alkynes

In the presence of a palladium catalyst and NaOAc, aryl iodides react with 1-aryl-1-alkynes to afford 9-alkylidene-9H-fluorenes in good yields. The products from this reaction are highly dependent on the base employed. This process appears to involve (1) oxidative addition of the aryl iodide to Pd(0), (2) alkyne insertion, (3) rearrangement of the resulting vinylic palladium intermediate to an arylpalladium species, and (4) aryl-aryl coupling with simultaneous regeneration of the Pd(0) catalyst. Consistent with this mechanism is the fact that 9-alkylidene-9H-fluorenes can also be prepared by the Pd-catalyzed rearrangement of 1,1-diaryl-2-iodo-1-alkenes.

Function of basonuclin in increasing transcription of the ribosomal RNA genes during mouse oogenesis

Active protein synthesis during early oogenesis requires accelerated transcription of ribosomal RNA genes (rDNAs). In response to this demand, rDNAs are amplified more than 1000-fold early in Xenopus oogenesis. Here, we report evidence that rDNA is not amplified in mouse oocytes, but these cells may instead employ the zinc-finger protein basonuclin, a putative rDNA transcription factor, to enhance rRNA synthesis. This conclusion is based on observations that basonuclin is localized in the nucleolus in the mouse oocyte early in its growth phase, when rRNA transcription is highly active; and that the binding sites of basonuclin zinc fingers on the human and mouse rDNA promoters are homologous. In a co-transfection assay, basonuclin can elevate transcription from an rDNA promoter, and its zinc-finger domain can inhibit RNA polymerase I transcription, as detected by a run-on assay, in growing mouse oocytes.