Abstract 5326: COSMIC: Enhancing the world's knowledge of somatic mutations in human cancer

COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://cancer.sanger.ac.uk) is the world's largest and most comprehensive online resource for exploring the impact of somatic mutations in human cancer. Now running for over 10 years, the 67th release (Oct 2013) describes 1592109 mutations in 947213 tumour samples across 25606 genes. This information is curated manually from the scientific literature, and automatically from genome resequencing consortium data portals. Full curation of the scientific literature provides in-depth understanding of the impact that each gene has in human cancer, and this has been achieved for 127 point-mutated cancer genes, and 185 fusion gene pairs. Curated genes are selected from the Cancer Gene Census (http://cancer.sanger.ac.uk/census), a listing of all genes with substantial evidence implicating them in cancer promotion, currently numbering 513 and updated frequently.

The mutations discovered in the re-sequencing of over 8000 tumour genomes are now present in COSMIC (viewable in isolation from the genic curations, http://cancer.sanger.ac.uk/wgs). In addition, the Sanger has now fully exome sequenced 1015 common cancer cell lines, identifying 1146874 coding mutations annotated for functional significance, and this is available exclusively in COSMIC at (http://cancer.sanger.ac.uk/cell_lines). While COSMIC has focused on point mutations and gene fusions, many other mutation mechanisms cause oncogenesis and these are now being integrated. The 67th COSMIC release includes copy number mutations integrated into the database and major web page views. To allow easy graphical examination of this data, copy number information was reduced to ‘gain’ and ‘loss’ annotations for inclusion in histograms and tables, with much more precise detail available with a further click. Copy number data is available in detail for every gene in COSMIC, and also for every tissue. Exploring cancer via COSMIC’s Cancer Browser (http://cancer.sanger.ac.uk/cosmic/browse/tissue), results not just in a plot of the most mutated genes, but now also a circular genome plot summarizing the copy number gains and losses across all the samples from that tumour type, all explorable in more detail via clicks on the pictures.

As the genomic data increases in COSMIC, it is becoming more important to qualitatively annotate the information, indicating which is more important or significant to oncogenesis. We are now building systems to better highlight known or putative functional mutations, improving the signal-to-noise ratio of cancer genome resequencing.

Citation Format: C Boutselakis, S A. Forbes, P Gunasekaran, M Jia, D Beare, N Bindal, C Y. Kok, K Leung, D Minjie, R Shepherd, S Bamford, S Ward, C Cole, J W. Teague, M Stratton, P Campbell, U McDermott. COSMIC: Enhancing the world's knowledge of somatic mutations in human cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5326. doi:10.1158/1538-7445.AM2014-5326

Relationships between the racemic structures of substituted mandelic acids containing 8- and 10-membered hydrogen bonded dimer rings

The structures of 27 monosubstituted mandelic acids, including several of their polymorphs, plus unsubstituted mandelic acid itself (two polymorphs) are investigated for structural similarity.

Involvement of interleukin-1 in the differentiation-inducing activity of tumor necrosis factor-alpha on a murine myeloid leukemia (WEHI-3B JCS)

We have shown previously that tumor necrosis factor-alpha (TNF-alpha) inhibits the growth and induces the differentiation of a murine myelomonocytic leukemia (WEHI-3B JCS cells) into macrophage-like cells. In this study, using reverse transcription polymerase chain reaction, we found that both endogenous interleukin-1 alpha and beta (IL-1 alpha, IL-1 beta) mRNA were up-regulated upon TNF-alpha induction. Exogenous IL-1 alpha and IL-1 beta also inhibited the growth as well as induced the differentiation of JCS cells, with IL-1 beta exerting a greater growth-inhibitory effect. Neutralizing anti-IL-1 alpha, anti-IL-1 beta and anti-TNF-alpha antibodies were further used to elucidate the role of IL-1 alpha, IL-1 beta and TNF-alpha in JCS cell differentiation. The results show that the IL-1 alpha-induced monocytic differentiation of JCS cells was effectively blocked by anti-IL-1 beta as well as anti-IL-1 beta antibodies and to a lesser extent by anti-TNF-alpha antibody. In contrast, the differentiation-inducing effect of IL-1 beta on JCS cells was only blocked by anti-IL-1 beta antibody but not by anti-IL-1 alpha or anti-TNF-alpha antibody. Finally, the TNF-alpha-induced monocytic differentiation of JCS cells was significantly blocked by anti-TNF-alpha and to a lesser extent by anti-IL-1 alpha and anti-IL-1 beta antibodies. Collectively, our results suggest that IL-1 beta alone may directly trigger JCS cell differentiation whereas the differentiation-inducing effect of IL-1 alpha may be via the endogenous production of IL-1 beta and/or TNF-alpha. In addition, IL-1 alpha and IL-1 beta may be involved, at least in part, in TNF-alpha-induced monocytic differentiation of the JCS leukemia cells.

A delivery system targeting bone formation surfaces to facilitate RNAi-based anabolic therapy

Metabolic skeletal disorders associated with impaired bone formation are a major clinical challenge. One approach to treat these defects is to silence bone-formation-inhibitory genes by small interference RNAs (siRNAs) in osteogenic-lineage cells that occupy the niche surrounding the bone-formation surfaces. We developed a targeting system involving dioleoyl trimethylammonium propane (DOTAP)-based cationic liposomes attached to six repetitive sequences of aspartate, serine, serine ((AspSerSer)(6)) for delivering siRNAs specifically to bone-formation surfaces. Using this system, we encapsulated an osteogenic siRNA that targets casein kinase-2 interacting protein-1 (encoded by Plekho1, also known as Plekho1). In vivo systemic delivery of Plekho1 siRNA in rats using our system resulted in the selective enrichment of the siRNAs in osteogenic cells and the subsequent depletion of Plekho1. A bioimaging analysis further showed that this approach markedly promoted bone formation, enhanced the bone micro-architecture and increased the bone mass in both healthy and osteoporotic rats. These results indicate (AspSerSer)(6)-liposome as a promising targeted delivery system for RNA interference-based bone anabolic therapy.

Sodium thiosulfate-based treatment in calcific uremic arteriolopathy: a consecutive case series

BACKGROUND

Calcific uremic arteriolopathy (CUA) is a rare complication in end stage renal disease with high mortality. Numerous case reports and one case series of 3 patients report the benefit of sodium thiosulfate (STS) for treatment of CUA. The purpose of this evaluation was to examine the response to a STS-based treatment approach in patients with CUA with 1 year follow up.

METHODS

A retrospective case series of 6 consecutive patients from Manitoba, Canada who met predefined diagnostic criteria for CUA and received STS between 2006 and 2008 were included. STS responders were defined as improvement in at least one of the following three parameters: pain severity, wound size and diagnostic imaging/radiography. Mortality, STS dose, duration, adverse events and cost were also collected.

RESULTS

Four patients were classified as responders. The 2 responders who survived at 1 year of follow-up demonstrated an improvement in all 3 parameters examined including an improvement in their follow-up diagnostic imaging results within the first 4 - 6 weeks of STS treatment. At 1 year of follow-up, 3 patients died.

CONCLUSION

Using an STS-based multifaceted treatment approach for CUA, 4 patients responded but 3 of 6 patients died within 1 year. Further larger prospective studies are needed to delineate STS responders from non-responders.

Symbiotic Characteristics of Rhizobium leguminosarum bv. trifolii Isolates Which Represent Major and Minor Nodule-Occupying Chromosomal Types of Field-Grown Subclover (Trifolium subterraneum L.)

The symbiotic effectiveness and nodulation competitiveness of Rhizobium leguminosarum bv. trifolii soil isolates were evaluated under nonsoil greenhouse conditions. The isolates which we used represented both major and minor nodule-occupying chromosomal types (electrophoretic types [ETs]) recovered from field-grown subclover (Trifolium subterraneum L.). Isolates representing four ETs (ETs 2, 3, 7, and 8) that were highly successful field nodule occupants fixed between 2- and 10-fold less nitrogen and produced lower herbage dry weights and first-harvest herbage protein concentrations than isolates that were minor nodule occupants of field-grown plants. Despite their equivalent levels of abundance in nodules on field-grown subclover plants, ET 2 and 3 isolates exhibited different competitive nodulation potentials under nonsoil greenhouse conditions. ET 3 isolates generally occupied more subclover nodules than isolates belonging to other ETs when the isolates were mixed in 1:1 inoculant ratios and inoculated onto seedlings. In contrast, ET 2 isolates were less successful at nodulating under these conditions. In many cases, ET 2 isolates required a numerical advantage of at least 6:1 to 11:1 to occupy significantly more nodules than their competitors. We identified highly effective isolates that were as competitive as the ET 3 isolates despite representing serotypes that were rarely recovered from nodules of field-grown plants. When one of the suboptimally effective isolates (ET2-1) competed with an effective and competitive isolate (ET31-5) at several different inoculant ratios, the percentages of nodules occupied by the former increased as its numerical advantage increased. Although subclover yields declined as nodule occupancy by ET2-1 increased, surprisingly, this occurred at inoculant ratios at which large percentages of nodules were still occupied by ET31-5.

Serological and Ecological Characteristics of a Nodule-Dominant Serotype from an Indigenous Soil Population of Rhizobium leguminosarum bv. trifolii

Although at least 13 antigenically distinct serotypes of Rhizobium leguminosarum bv. trifolii exist in an Abiqua silty clay loam soil, one serotype, AS6, occupies >/=50% of the root nodules formed on field-grown subclover and between 33 and 78% of the nodules formed on five annual clover species grown in the same soil under laboratory conditions. The dominance of subclover nodules by serotype AS6 was reproducible over a 4-year sampling period and throughout the entire 200- by 100-m pasture examined. Serotype AS6 was composed of three antigenically distinct subtypes (AS6-a, AS6-b, and AS6-c). Each subtype contributed about one-third of the AS6 isolates recovered from nodules of field-grown subclover plants and maintained similar population densities in nonrhizosphere and rhizosphere soil. Rhizobia with the AS6 antigenic signature accounted for from 20 to 100% of the soil populations of R. leguminosarum in arable and pasture soils under legumes throughout the state of Oregon. Over a 12-month period, the population densities of the serotype AS6 complex and three minor nodule-occupying serotypes (AG4, AP17, and AS21) were measured in the rhizospheres of field-grown subclover and orchard grass and in nonrhizosphere Abiqua soil. Regardless of season or serotype, the orchard grass rhizosphere effect was minimal, with the ratio between rhizosphere and nonrhizosphere serotype population densities ranging between 2.5 (midsummer) and 10.5 (spring). In contrast, the magnitude of the subclover rhizosphere effect varied seasonally and among serotypes. Between October and December the ratios for all serotypes were similar (12.5 to 25.5). However, in the spring (April and May), the magnitude of the rhizosphere effect varied among the indigenous serotypes (ratios, 10.5 to 442) and for minor nodule-occupying serotypes AS21 (ratio, 442) and AP17 (ratio, 47) was as great as, or even greater than, the magnitude of the rhizosphere effect observed with the AS6 complex (ratio, 65.5).

Epimedium-derived flavonoids promote osteoblastogenesis and suppress adipogenesis in bone marrow stromal cells while exerting an anabolic effect on osteoporotic bone

BACKGROUND

Epimedium-derived flavonoids (EFs) have been reported to prevent bone loss in ovariectomized (OVX) rats and late postmenopausal women but the underlying mechanism of the anabolic effect is unknown.

OBJECTIVE

This study aimed to investigate the effect of EFs on osteoporotic bone using histomorphometry and on osteoblastogenesis/adipogenesis of bone marrow stromal cells (BMSCs).

METHODS

11-month-old female Wistar rats were divided into Sham, OVX, Sham+soluble vehicle (Sham+SV), OVX+SV and OVX+EFs (10 mg/kg/day) groups. 3 months after surgery, rats from the first two groups were euthanized to verify the establishment of OVX-induced osteoporosis. Other groups were orally treated with either daily SV or EFs for 4 months. At sacrifice, serum was analyzed for the levels of osteocalcin and TRACP 5b, BMD in the proximal femur was measured by pQCT. Static and dynamic bone histomorphometry was performed in proximal tibiae with microCT and undecalcified sections, respectively. The effect of EF treatment on differentiation of rat BMSCs was assessed by colony formation assays and gene expression analysis, respectively. Gene expression, ALP activity and adipocyte numbers were determined in differentiating human BMSCs after exposure to conditioned serum from SV- or EFs-treated OVX rats.

RESULTS

The serum level of osteocalcin was higher and TRACP 5b was lower in EFs versus SV-treated OVX rats. BMD, BV/TV, Tb.N and Conn.D in EFs-treated OVX rats were significantly greater than those of SV-treated OVX rats. Bone histomorphometric parameters OS/BS, MAR, and BFR/BS were significantly higher in EFs versus SV-treated OVX rats. EFs significantly increased osteogenesis and decreased adipogenesis of BMSCs, as evidenced by CFU-ALP and CFU-Adipo assays, respectively. The mRNA level of Runx2 and bone sailoprotein was significantly higher while PPARgamma2 was significantly lower in BMSCs from EFs-treated versus SV-treated OVX rats. ALP activity and Runx2 mRNA was significantly higher while adipocyte number and PPARgamma2 mRNA was significantly lower in human BMSCs after exposure to conditioned serum from EFs versus SV-treated OVX rats.

CONCLUSION

EFs exerted anabolic effect on osteoporotic bone by concomitantly promoting osteogenic and suppressing adipogenic differentiation of BMSCs.

Freezing inactivation of Escherichia coli and Enterococcus faecalis in water: response of different strains

The effect of freezing temperature (-7, -15, -30 and -80 degrees C), number of freeze/thaw cycles (1 to 5 cycles) and sample volume (100 mL and 100 microL) on the viability of a pathogenic and an opportunistically pathogenic Escherichia coli, a vancomycin-resistant and a vancomycin-sensitive Enterococcus faecalis were examined. About 3.3 to 4.3 and 1.5 to 2.4 log reduction in cell density were observed in E. coli and E. faecalis, respectively, in the 100 mL samples frozen at -30 degrees C or warmer. Freezing at -80 degrees C was the least effective in killing the microbes, on average the log reduction at -80 degrees C was approximately 1.0 to 1.5 units less than those achieved at the three warmer temperatures. Based on statistical analysis, cell inactivation levels achieved at -7, -15, or -30 degrees C were not significantly different (P-value = 0.1648). There were no statistical difference in terms of log reduction obtained under all experimental conditions for the two E. coli strains (P-value = 0.46) and the two E. faecalis strains (P-value = 0.10). The number of freezing/thaw cycles and sample volume, however, profoundly affected inactivation capacity of freezing. Freezing could be an effective method for further reduction of E. coli and Enterococcus in municipal wastewater/sludge.

Identification of genes responsive to low-intensity pulsed ultrasound stimulations

This study was designed to compare the temporal changes of gene expression profile in osteoblastic cell lines (SaOS-2) treated with low-intensity pulsed ultrasound stimulation (LIPUS) using complementary DNA (cDNA) microarrays. SaOS-2 cells were treated with LIPUS for 20min. Thereafter, cells were harvested and RNA was extracted twice at 4 and 24h, respectively. Using cDNA microarrays, 7488 genes with changes in expression in SaOS-2 cells were identified for comparison. Microarray analysis revealed a total of 165 genes in SaOS-2 cells were regulated at 4 and 24h after LIPUS treatment. Except for 30 known LIPUS-regulated genes, our study demonstrated for the first time that over 100 genes were related to the underlying molecular mechanism of LIPUS and suggested that LIPUS might regulate a transient expression of numerous critical genes in osteoblastic cells. These results provide further understanding of the role of LIPUS in the regulation of osteoblastic gene expression potentially involved in the molecular mechanism of osteogenesis in fracture repair.

Low-intensity pulsed ultrasound accelerated bone-tendon junction healing through regulation of vascular endothelial growth factor expression and cartilage formation

The purpose of this study was to use our established partial patellectomy rabbit model to study the effects of low-intensity pulsed ultrasound (LIPUS) on patella-patellar tendon (PPT) junction repair through hypothesized pathways including regulation of vascular endothelial growth factor (VEGF) and chondrogenesis. Standard partial patellectomy was conducted in sixty-four 18 wk-old rabbits that were subsequently divided into LIPUS and control group. The PPT complex was harvested at week 2, 4, 8 and 16 postoperatively (n = 8 for each time point) for preparation of sagittal sections that were evaluated for angiogenesis by analyzing VEGF expression and chondrogenesis. Results showed differences in the pattern of VEGF expression between LIPUS and control groups during the entire healing process, i.e., significant differences in the average percentage of VEGF expression found in between the LIPUS and the control groups. At postoperative week 4, the chondrocytes and osteoblasts in woven bone expressed significantly more VEGF in the LIPUS group than that in the control group (35.6% +/- 7.0% versus 28.0% +/- 4.6%, p < 0.05). Compared with the control group, the development of cartilaginous metaplasia was found more advanced in the scar tissue next to the articular cartilage of the remaining patella in the LIPUS group that was expressed with VEGF in the chondrocytes (38.8% +/- 12.3%). However, the specimens in the control group just showed the similar cartilaginous metaplasia region until postoperative week 8. Histomorphometry revealed thicker fibrocartilage zone and larger cartilaginous metaplasia field at PPT healing interface in LIPUS group compared with those of the control group at week 8 and 16. In conclusion, this was the first quantitative study to demonstrate that LIPUS improved B-T junction healing through regulation of VEGF expression in early healing phase and subsequent chondrogenesis.