Triply Interlocked [2]catenanes: Rational Synthesis, Reversible Conversion Studies and Unprecedented Application in Photothermal Responsive Elastomer.

Triply interlocked [2]catenane complexes featuring two identical, mechanically interlocked units are extraordinarily rare chemical compounds, whose properties and applications remain open to detailed studies. Herein, we introduce the rational design of a new ligand precursor, L1, suitable for the synthesis of six triply interlocked [2]catenanes by coordination-driven self-assembly. The interlocked compounds can be reversibly converted into the corresponding simple triangular prism metallacage by addition of H2O or DMF solvents to their CH3OH solutions, thereby demonstrating the importance of π⋅⋅⋅π stacking and hydrogen bonding interactions in the formation of triply interlocked [2]catenanes. Moreover, extensive studies have been conducted to assess the remarkable photothermal conversion performance. Complex 6 a, exhibiting outstanding photothermal conversion performance (conversion efficiency in solution : 31.82 %), is used to prepare novel photoresponsive elastomer in combination with thermally activated liquid crystal elastomer. The resultant material displays robust response to near-infrared (NIR) laser and the capability of completely reforming the shape and reversible actuation, paving the way for the application of half-sandwich organometallic units in photo-responsive smart materials.

Diabetic Retinopathy and Brain Structure, Cognition Function, and Dementia: A Bidirectional Mendelian Randomization Study.

BACKGROUND: Accumulating evidence has demonstrated that hyperglycemia is a possible risk factor for mild cognitive impairment or Alzheimer's disease. Diabetic retinopathy (DR) has been identified as a risk factor for dementia in patients with diabetes. OBJECTIVE: This study aimed to investigate the causal relationships between DR and brain structure, cognitive function, and dementia. METHODS: We performed bidirectional two-sample Mendelian randomization for DR, brain structure, cognitive function, and dementia using the inverse-variance weighted method. RESULTS: Inverse-variance weighted analysis showed the association of DR with vascular dementia (OR = 1.68, 95% CI: 1.01-2.82), and dementia was significantly associated with the increased risk of non-proliferative DR (NPDR) (OR = 1.76, 95% CI: 1.04-2.98). Furthermore, better cognitive performance was significantly associated with a reduced risk of NPDR (OR = 0.85, 95% CI: 0.74-0.98). No association was observed between DR and brain structure. CONCLUSIONS: These findings suggest that the association of DR with vascular dementia. The reciprocal effect of cognitive performance and dementia on NPDR risk highlights the potential benefits of dementia prevention for reducing the burden of DR.

Self-Assembly and Photothermal Conversion of MetallaRussian Doll and Metalla[2]catenanes Induced via Multiple Stacking Interactions.

A variety of organometallic supramolecular architectures have been constructed over the past decades and their properties were also explored via different strategies. However, the synthesis of metalla-Russian doll is still a fascinating challenge. Herein, a series of new coordination supramolecular complexes, including a metalla-Russian doll, metalla[2]catenanes, and metallarectangles, were synthesized by using meticulously selected Cp*Rh (Cp* = η5-C5Me5) building units (E1, E2, and E3) and three rigid anthracylpyridine ligands (L1, L2, and L3) via a self-assembly strategy. While the combination of the short ligand L1 and E1 or E2 generated two metallarectangles, the longer ligand L2 containing an alkynyl group resulted in two new [2]catenanes, most likely due to which the strong electron-donating effect of alkynyl groups causes self-accumulation. Interestingly, an unusual Russian doll assembly was obtained through the reaction of L3 and E3 based on sextuple π···π stacking interactions. Furthermore, the dynamic structural conversion between [2]catenanes and the corresponding metallarectangles could be observed through concentration-, solvent-, and guest-induced effects. The [2]catenane complexes 4b displayed efficient photothermal conversion efficiency in solution (20.2%), in comparison with other organometallic macrocycles. We believe that π···π stacking interactions generate active nonradiative pathways and promote radiative photodeactivation pathways. This study proves the versatility of half-sandwich building units, not only to build complicated supramolecular topologies but also in effective functional materials for various appealing applications.

Predicted lean body mass in relation to cognitive function in the older adults.

Background: Previous findings about lean body mass (LBM) and cognitive function remain unclear. We aimed to examine this association by using data from the National Health and Nutrition Examination Survey (NHANES). Methods: Using data from the NHANES 2011-2014, we conducted logistic regression models to investigate the relation between the predicted LBM and domain-specific cognitive function assessed by Digit Symbol Substitution Test (DSST), Consortium to Establish a Registry for Alzheimer's Disease Word Learning test (CERAD-WL) and Delayed Recall test (CERAD-DR), and Animal Fluency (AF) for information processing speed, memory, and executive function, respectively. Cognitive impairment was defined as the lowest quartile of each cognitive test in the total population. Sex-stratified analysis was further made. Results: A total of 2955 participants aged 60 and above (mean [SD] age, 69.17[0.20] years; 1511 female [51.13%]) were included in the study. After being adjusted for social economic factors, anthropometric parameters, and diseases, we found a positive association between predicted LBM and information processing speed (Odds ratio of DSST impairment= 0.95, 95%CI= 0.91 to 0.99) regardless of body mass index and sex. Compared with patients in the first quartile of predicted LBM, those in the fourth quartile had an odds ratio of 0.355 (95% confidence interval 0.153-0.822) for DSST impairment. No significant relation in other cognitive tests and predicted LBM was found whether stratified by sex or not. Conclusion: Our findings point to the association between predicted lean body mass and cognitive dysfunction in information processing speed, which could be used for early detection and prevention of deterioration of cognitive function among older adults.

Relationship Between Weight-Change Patterns and Cognitive Function: A Retrospective Study.

BACKGROUND: Obesity has been linked to cognitive impairment. However, how changes in body mass index (BMI) over the life course influence cognitive function remains unclear. OBJECTIVE: The influence of distinct weight-change patterns from young adulthood to midlife and late adulthood on cognitive function in older adults was explored. METHODS: A total of 5,809 individuals aged≥60 years were included and categorized into four groups on the basis of BMI change patterns. Cognitive function was assessed using four cognition tests in the baseline survey. The relationship between the weight-change patterns and cognition was evaluated using regression models. RESULTS: In comparison with participants who remained at non-obese, those moving from the non-obese to obese weight-change pattern from young (25 years of age) to middle adulthood showed lower Digit Symbol Substitution Test (DSST) scores (ß= -1.28; 95% confidence interval [CI]: -2.24 to -0.32). A non-obese to obese change pattern from age 25 years of age to 10 years before baseline was associated with a higher risk of DSST impairment (odds ratio = 1.40; 95% CI: 1.09 to 1.79). In comparison with participants whose heaviest weight was recorded after 60 years of age, those with the heaviest weight between 18 and 40 years of age had lower DSST scores (ß= -1.46; 95% CI: -2.77 to -1.52). CONCLUSION: Our results suggest that the transition from the non-obese to obese category in early adulthood and appearance of the heaviest weight between 18 and 40 years of age are associated with lower cognitive function in later life.

Straight-segment mandibulectomy: a reproducible porcine mandibular critical-size defect model.

Porcine mandibular defect models are commonly used for the preclinical evaluation of reconstruction techniques. Existing studies vary in technique, complexity, and postoperative outcomes. The procedures are complex and often described without sufficient detail. We describe in detail a simple and reproducible method for creating a critical-size mandibular defect in a porcine model. Seven hemimandibular critical size defects were created in five male Yorkshire-Landrace pigs, three with unilateral defects and two with bilateral defects. A transverse incision was made over the mandibular body. Periosteum was incised and elevated to expose the mandibular body and a critical-size defect of 30 × 20 mm created using an oscillating saw. The implant was inserted and fixed with a titanium reconstruction plate and bicortical locking screws, and the wound closed in layers with resorbable sutures. Intraoral contamination was avoided. Dentition was retained and the mental nerve and its branches preserved. The marginal mandibular nerve was not encountered during dissection. All pigs retained normal masticatory function, and there were no cases of infection, wound breakdown, haematoma, salivary leak, or implant-related complications. The procedure can be performed bilaterally on both hemimandibles without affecting load-bearing function. All pigs survived until the end point of three months. Postoperative computed tomographic scans and histology showed new bone formation, and a three-point bend test showed the restoration of biomechanical strength. Straight-segment mandibulectomy is a simple and reproducible method for the creation of critical-size mandibular defects in a porcine model, simulating a load-bearing situation.

Association of kidney function and brain health: A systematic review and meta-analysis of cohort studies.

OBJECTIVE: This study aimed to evaluate the bidirectional association between the kidney dysfunction and the brain health, including structural and functional abnormalities. DESIGN: Systematic review and meta-analysis with network meta-analysis for outcomes with different estimated glomerular filtration rate (eGFR) ranges. DATA SOURCES: PubMed, Embase database, Cochrane library and Web of Science (up to Dec. 2021). ELIGIBILITY CRITERIA FOR SELECTING STUDIES: Longitudinal studies that provided evidence of the impact of kidney function estimated from eGFR and urine albumin-to-creatinine ratio (UACR) or chronic kidney disease (CKD) on structural and functional brain abnormalities, and those that provided evidence of the opposite relationship. Studies with study population mean age under 18 years old were excluded. MAIN OUTCOME MEASURES: Two independent reviewers screened the included studies, extracted the data, and assessed the risk of bias. We performed a random-effects meta-analysis and a network meta-analysis for outcomes with compatible data. We assessed the risk of bias using the Newcastle-Ottawa Quality Assessment Scale criteria (NOS). Subgroup and sensitivity analyses were conducted to explore heterogeneity in the meta-analyses. Inconsistency analyses using the node-splitting method were performed to confirm the results of network meta-analysis. RESULTS: A total of 53 studies with 3037,357 participants were included in the current systematic review. Among these, 16 provided evidence of structural brain abnormalities, and 38 provided evidence of cognitive impairment and dementia. Analysis of evidence of categorical kidney function showed a positive association between kidney dysfunction and cerebral small vessel disease (cSVD) (relative risk (RR) 1.77, 95% confidence interval (CI) 1.40-2.24, I2 = 0.0%), but such results were not found in the analyses of evidence where the kidney function was measured as a continuous variable. Meanwhile, analysis of 28 prior longitudinal studies with 194 compatible sets of data showed that the worse kidney function as categorical variables was related to a greater risk of global brain cognitive disorder (RR 1.28, 95% CI 1.20-1.36, I2 = 82.5%). CONCLUSIONS: In this systematic review and meta-analysis, we found a positive association between CKD and functional brain disorders. However, the relationship between the kidney dysfunction and structural abnormalities in the brain remains controversial. As for the opposite relationship, structural brain abnormalities, especially cerebral microbleeds and silent infarction, but not functional brain abnormalities, are associated with worse renal function. In addition, a higher UACR, but not a lower eGFR, was associated with a higher risk of Alzheimer's disease and vascular dementia.

Cerebral Blood Flow Alterations and Obesity: A Systematic Review and Meta-Analysis.

BACKGROUND: Reduction in cerebral blood flow (CBF) plays an essential role in the cognitive impairment and dementia in obesity. However, current conclusions regarding CBF changes in patients with obesity are inconsistent. OBJECTIVE: A systematic review and meta-analysis was performed to evaluate the relationship between obesity and CBF alterations. METHODS: We systematically screened published cross-sectional and longitudinal studies focusing on the differences in CBF between obese and normal-weight individuals. Eighteen studies including 24,866 participants, of which seven articles reported longitudinal results, were evaluated in the present study. RESULTS: The results of the meta-analysis showed that in cross-sectional studies, body mass index (BMI) was negatively associated with CBF (ß= -0.31, 95% confidence interval [CI]: -0.44, -0.19). Moreover, this systematic review demonstrated that obese individuals showed global and regional reductions in the CBF and increased CBF in diverse functional areas of the frontal lobe, including the prefrontal cortex, left frontal superior orbital, right frontal mid-orbital cortex, and left premotor superior frontal gyrus. CONCLUSION: Our findings suggest that BMI, rather than waist circumference and waist-to-hip ratio, is inversely associated with CBF in cross-sectional studies. The CBF of obese individuals showed global and regional reductions, including the frontal lobe, temporal and parietal lobes, cerebellum, hippocampus, and thalamus.

Association of Sarcopenia and A Body Shape Index With Overall and Cause-Specific Mortality.

Aim: This observational study aimed to examine the association between the A Body Shape Index (ABSI) and/or sarcopenia and total, cardiovascular, and cancer mortality. Methods: The associations of sarcopenia and ABSI with all-cause, cardiovascular, and cancer mortality were assessed in 4,488 participants from the 1999-2004 National Health and Nutrition Examination Survey (NHANES) who were followed up until December 31, 2015. Models were analyzed separately for men and women and adjusted for age, race, and other confounding factors. ABSI was assessed as a continuous measurement by quartile for men and women. Population attributable fractions (PAFs) were calculated to assess mortality caused by sarcopenia and/or ABSI in the study population. Results: When ABSI was assessed as a continuous variable, the ABSI quartile showed a linear trend for total (p = 0.0001), cardiovascular (p = 0.04), and cancer (p = 0.02) mortality in men and for total (p = 0.06) and cardiovascular (p = 0.06) mortality in women. The hazard ratios (HRs) of the fourth ABSI quartile were 1.51 [95% confidence interval (CI): 1.20-1.89] in men and 1.23 (95% CI: 0.93-1.64) in women, compared with those in the first quartile. When ABSI was assessed by quartile, the appendicular skeletal mass index (ASMI) was lower in the groups with high ABSI. When high ABSI was combined with sarcopenia, the HRs of all-cause mortality were 2.05 (95% CI: 1.60-2.62) in men and 1.51 (95% CI: 1.19-1.92) in women. In the subpopulation (sarcopenia group or higher ABSI), the PAFs of mortality due to sarcopenia were 26.16% (95% CI: 12.68-37.56) in men and 21.89% (95% CI: 5.64-35.35) in women, and the PAF of mortality due to higher ABSI was 23.70% (95% CI: 12.11-33.77) in men. Conclusion: The ABSI value was significantly associated with all-cause and cardiovascular mortality, and the co-existence of higher ABSI values and sarcopenia can contribute to a more significant death risk in comparison with high ABSI values or sarcopenia. Moreover, the ABSI values in combination with the ASMI can be used to preliminarily evaluate the content and distribution of fat and muscle and to predict the risk of death in obese and sarcopenic populations.

Association Between Diabetic Retinopathy, Brain Structural Abnormalities, and Cognitive Impairment for Accumulated Evidence in Observational Studies.

PURPOSE: To evaluate the association between diabetic retinopathy (DR) and cerebral disease or cognitive impairment. DESIGN: Systematic review and meta-analysis. METHOD: The hypothesis was formulated prior to data collection. Cross-sectional studies and cohort studies that assessed the association between any measure of DR and cerebral small vessel disease or any type of cognitive impairment in diabetic participants were included. The data were independently extracted by two investigators. This systematic review and meta-analysis adhered to the Preferred Reporting Items for Systematic Reviews and Meta-analyses and Meta-analysis of Observational Studies in Epidemiology guidelines RESULTS: A total of 27 studies were included. The combined odds ratio of 5 cross-sectional/cohort studies that reported that the associations between DR and cerebral structural changes was 1.75 (95% confidence interval [CI]: 1.36-2.25). The combined hazard ratio of 4 cohort studies that examined the association between DR and cognitive impairment events was 1.47 (95% CI: 1.22-1.78). The combined odds ratio of 14 cross-sectional/cohort studies that examined the association between DR and different cognitive impairment events was 1.43 (95% CI: 1.06-1.93). The overall coefficient (ß) of 4 studies that examined the relationship between DR and specific cognitive performance was 0.09 (95% CI: 0.00-0.18). Considering the quality of the data, we have performed subgroup analysis in studies scored >7 and studies scored ≤7, respectively, according to the Newcastle-Ottawa scale. CONCLUSION: The present meta-analysis suggests that DR is associated with an increased risk of structural abnormalities in the brain and cognitive impairment. This association remained significant after adjusting for blood glucose, and the presence of hypertension, indicating that DR is an important danger signal for cerebral abnormalities.

The Association Between Diabetes Mellitus and Risk of Sarcopenia: Accumulated Evidences From Observational Studies.

Aim: We performed a meta-analysis of observational studies to evaluate the association between the presence of sarcopenia and HbA1c, prediabetes, diabetes and diabetic complications. Method: The PubMed, Embase, Cochrane and Web of Science databases were searched from inception to May 2021. We included full-text English language articles that reported the prevalence of sarcopenia in patients with and without diabetes. Quality assessment was performed according to the Newcastle- Ottawa scale for observational studies. Results: Sixteen studies were included in the meta-analysis. Three studies showed that high HbA1c levels lead to loss of muscle mass, and one study involving prediabetes showed that people with prediabetes had lower muscle mass, strength, and performance than non-diabetic population. Seven studies showed that people with diabetes had a higher risk of sarcopenia than those without diabetes (combined OR: 2.09, 95% CI:1.62-2.70). The remaining five studies suggested that diabetic complications increased the risk of sarcopenia (combined OR: 2.09,95% CI:1.62-2.70). Conclusion: High HbA1c levels, prediabetes, diabetes and diabetes complications were associated with an increased risk of sarcopenia. Therapeutic strategies addressed to avoid the conversion of IGT to diabetes and to optimize glycemic control are warranted to prevent or arrest sarcopenia in the diabetic population.

COSMIC: the Catalogue Of Somatic Mutations In Cancer.

COSMIC, the Catalogue Of Somatic Mutations In Cancer (https://cancer.sanger.ac.uk) is the most detailed and comprehensive resource for exploring the effect of somatic mutations in human cancer. The latest release, COSMIC v86 (August 2018), includes almost 6 million coding mutations across 1.4 million tumour samples, curated from over 26 000 publications. In addition to coding mutations, COSMIC covers all the genetic mechanisms by which somatic mutations promote cancer, including non-coding mutations, gene fusions, copy-number variants and drug-resistance mutations. COSMIC is primarily hand-curated, ensuring quality, accuracy and descriptive data capture. Building on our manual curation processes, we are introducing new initiatives that allow us to prioritize key genes and diseases, and to react more quickly and comprehensively to new findings in the literature. Alongside improvements to the public website and data-download systems, new functionality in COSMIC-3D allows exploration of mutations within three-dimensional protein structures, their protein structural and functional impacts, and implications for druggability. In parallel with COSMIC's deep and broad variant coverage, the Cancer Gene Census (CGC) describes a curated catalogue of genes driving every form of human cancer. Currently describing 719 genes, the CGC has recently introduced functional descriptions of how each gene drives disease, summarized into the 10 cancer Hallmarks.

Preliminary structural characterization and hypoglycemic effects of an acidic polysaccharide SERP1 from the residue of Sarcandra glabra.

An acidic polysaccharide (SERP1) was isolated from the residue of Sarcandra glabra (Thunb.) Nakai by water extraction and purified by decoloration and ion exchange chromatography. The structure of SERP1 was determined by HPLC, HPSEC-MALLS, FT-IR, and NMR. The results indicated that SERP1 was a homogeneous heteropolysaccharide with the absolute molecular weight of 4.208×104Da in the aqueous phase. 1,4-linked α-d-galacturonic acid, methyl esterified 1,4-linked α-d-galacturonic acid, 1,4-linked α-d-glucuronic acid, 1,5-linked α-l-arabinose, 1,3-linked ß-d-galactose 1,4-linked α-d-glucose, 1,4,6-linked ß-d-glucose, 1,6-linked ß-d-glucose, and 1,2-linked rhamnose existed in SERP1. In vitro α-glucosidase inhibition assay indicated that SERP1 had a low IC50 value of 49.01µg/mL, which exhibited stronger α-glucosidase enzyme inhibitory activity than acarbose at the same concentration. The treatment of SERP1 to type 2 diabetes mellitus mice alleviated the hyperglycemia, increased glucose utilization of peripheral tissues of the liver and inhibited the liver injury. This study provides a possible exploration to use valuable industrial waste.

COSMIC: somatic cancer genetics at high-resolution.

COSMIC, the Catalogue of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk) is a high-resolution resource for exploring targets and trends in the genetics of human cancer. Currently the broadest database of mutations in cancer, the information in COSMIC is curated by expert scientists, primarily by scrutinizing large numbers of scientific publications. Over 4 million coding mutations are described in v78 (September 2016), combining genome-wide sequencing results from 28 366 tumours with complete manual curation of 23 489 individual publications focused on 186 key genes and 286 key fusion pairs across all cancers. Molecular profiling of large tumour numbers has also allowed the annotation of more than 13 million non-coding mutations, 18 029 gene fusions, 187 429 genome rearrangements, 1 271 436 abnormal copy number segments, 9 175 462 abnormal expression variants and 7 879 142 differentially methylated CpG dinucleotides. COSMIC now details the genetics of drug resistance, novel somatic gene mutations which allow a tumour to evade therapeutic cancer drugs. Focusing initially on highly characterized drugs and genes, COSMIC v78 contains wide resistance mutation profiles across 20 drugs, detailing the recurrence of 301 unique resistance alleles across 1934 drug-resistant tumours. All information from the COSMIC database is available freely on the COSMIC website.

Structure, chain conformation, and immunomodulatory activity of the polysaccharide purified from Bacillus Calmette Guerin formulation.

A polysaccharide, coded as BDP, purified from the injection powder of Bacillus Calmette Guerin (BCG) polysaccharide and nucleic acid, was composed mainly of α-D-(1→4)-linked glucan with (1→6)-linked branches and trace amounts of fucose and mannose from the results of FT-IR, HPAEC-PAD and NMR spectrum. The Mw, Mn, Mz, and [Formula: see text] were determined to be 1.320×10(5)g/mol, 1.012×10(5)g/mol, 2.139×10(5)g/mol, and 21.8±3.2%nm by using HPSEC-MALLS, respectively. The ν value from [Formula: see text] was calculated to be 0.52±0.01, which firstly clarified that BDP existed as random coils in 0.9% NaCl aqueous solution. AFM and SEM combined with Congo-red test also revealed that the polysaccharide was irregular globular like or curly structure. Furthermore, in vitro tests on RAW264.7 murine macrophages cells revealed that BDP exhibited significant immunomodulatory activity.

An FDA-Drug Library Screen for Compounds with Bioactivities against Meticillin-Resistant Staphylococcus aureus (MRSA).

The lack of new antibacterial drugs entering the market and their misuse have resulted in the emergence of drug-resistant bacteria, posing a major health crisis worldwide. In particular, meticillin-resistant Staphylococcus aureus (MRSA), a pathogen responsible for numerous human infections, has become endemic in hospitals worldwide. Drug repurposing, the finding of new therapeutic indications for approved drugs, is deemed a plausible solution to accelerate drug discovery and development in this area. Towards this end, we screened 1163 drugs approved by the Food and Drug Administration (FDA) for bioactivities against MRSA in a 10 µM single-point assay. After excluding known antibiotics and antiseptics, six compounds were identified and their MICs were determined against a panel of clinical MRSA strains. A toxicity assay using human keratinocytes was also conducted to gauge their potential for repurposing as topical agents for treating MRSA skin infections.

COSMIC: exploring 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 resource for exploring the impact of somatic mutations in human cancer. Our latest release (v70; Aug 2014) describes 2 002 811 coding point mutations in over one million tumor samples and across most human genes. To emphasize depth of knowledge on known cancer genes, mutation information is curated manually from the scientific literature, allowing very precise definitions of disease types and patient details. Combination of almost 20,000 published studies gives substantial resolution of how mutations and phenotypes relate in human cancer, providing insights into the stratification of mutations and biomarkers across cancer patient populations. Conversely, our curation of cancer genomes (over 12,000) emphasizes knowledge breadth, driving discovery of unrecognized cancer-driving hotspots and molecular targets. Our high-resolution curation approach is globally unique, giving substantial insight into molecular biomarkers in human oncology. In addition, COSMIC also details more than six million noncoding mutations, 10,534 gene fusions, 61,299 genome rearrangements, 695,504 abnormal copy number segments and 60,119,787 abnormal expression variants. All these types of somatic mutation are annotated to both the human genome and each affected coding gene, then correlated across disease and mutation types.

Data mining using the Catalogue of Somatic Mutations in Cancer BioMart.

Catalogue of Somatic Mutations in Cancer (COSMIC) (http://www.sanger.ac.uk/cosmic) is a publicly available resource providing information on somatic mutations implicated in human cancer. Release v51 (January 2011) includes data from just over 19,000 genes, 161,787 coding mutations and 5573 gene fusions, described in more than 577,000 tumour samples. COSMICMart (COSMIC BioMart) provides a flexible way to mine these data and combine somatic mutations with other biological relevant data sets. This article describes the data available in COSMIC along with examples of how to successfully mine and integrate data sets using COSMICMart. DATABASE URL: http://www.sanger.ac.uk/genetics/CGP/cosmic/biomart/martview/.

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.

COSMIC (http://www.sanger.ac.uk/cosmic) curates comprehensive information on somatic mutations in human cancer. Release v48 (July 2010) describes over 136,000 coding mutations in almost 542,000 tumour samples; of the 18,490 genes documented, 4803 (26%) have one or more mutations. Full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs (19 new cancer genes and 30 new fusion pairs this year) and this number is continually increasing. Key amongst these is TP53, now available through a collaboration with the IARC p53 database. In addition to data from the Cancer Genome Project (CGP) at the Sanger Institute, UK, and The Cancer Genome Atlas project (TCGA), large systematic screens are also now curated. Major website upgrades now make these data much more mineable, with many new selection filters and graphics. A Biomart is now available allowing more automated data mining and integration with other biological databases. Annotation of genomic features has become a significant focus; COSMIC has begun curating full-genome resequencing experiments, developing new web pages, export formats and graphics styles. With all genomic information recently updated to GRCh37, COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources.

Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes.

Clear cell renal cell carcinoma (ccRCC) is the most common form of adult kidney cancer, characterized by the presence of inactivating mutations in the VHL gene in most cases, and by infrequent somatic mutations in known cancer genes. To determine further the genetics of ccRCC, we have sequenced 101 cases through 3,544 protein-coding genes. Here we report the identification of inactivating mutations in two genes encoding enzymes involved in histone modification-SETD2, a histone H3 lysine 36 methyltransferase, and JARID1C (also known as KDM5C), a histone H3 lysine 4 demethylase-as well as mutations in the histone H3 lysine 27 demethylase, UTX (KMD6A), that we recently reported. The results highlight the role of mutations in components of the chromatin modification machinery in human cancer. Furthermore, NF2 mutations were found in non-VHL mutated ccRCC, and several other probable cancer genes were identified. These results indicate that substantial genetic heterogeneity exists in a cancer type dominated by mutations in a single gene, and that systematic screens will be key to fully determining the somatic genetic architecture of cancer.