Databases and QSAR for Cancer Research

In this review, we take a survey of bioinformatics databases and quantitative structure-activity relationship studies reported in published literature. Databases from the most general to special cancer-related ones have been included. Most commonly used methods of structure-based analysis of molecules have been reviewed, along with some case studies where they have been used in cancer research. This article is expected to be of use for general bioinformatics researchers interested in cancer and will also provide an update to those who have been actively pursuing this field of research

Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes

The Network of Cancer Genes (NCG) collects and integrates data on 736 human genes that are mutated in various types of cancer. For each gene, NCG provides information on duplicability, orthology, evolutionary appearance and topological properties of the encoded protein in a comprehensive version of the human protein-protein interaction network. NCG also stores information on all primary interactors of cancer proteins, thus providing a complete overview of 5357 proteins that constitute direct and indirect determinants of human cancer. With the constant delivery of results from the mutational screenings of cancer genomes, NCG represents a versatile resource for retrieving detailed information on particular cancer genes, as well as for identifying common properties of precompiled lists of cancer genes. NCG is freely available at: http://bio.ifom-ieo-campus.it/ncg

The cellular and molecular carcinogenic effects of radon exposure: a review.

Journal ArticleResearch Support, Non-U.S. Gov'tReviewOpen access articleRadon-222 is a naturally occurring radioactive gas that is responsible for approximately half of the human annual background radiation exposure globally. Chronic exposure to radon and its decay products is estimated to be the second leading cause of lung cancer behind smoking, and links to other forms of neoplasms have been postulated. Ionizing radiation emitted during the radioactive decay of radon and its progeny can induce a variety of cytogenetic effects that can be biologically damaging and result in an increased risk of carcinogenesis. Suggested effects produced as a result of alpha particle exposure from radon include mutations, chromosome aberrations, generation of reactive oxygen species, modification of the cell cycle, up or down regulation of cytokines and the increased production of proteins associated with cell-cycle regulation and carcinogenesis. A number of potential biomarkers of exposure, including translocations at codon 249 of TP53 in addition to HPRT mutations, have been suggested although, in conclusion, the evidence for such hotspots is insufficient. There is also substantial evidence of bystander effects, which may provide complications when calculating risk estimates as a result of exposure, particularly at low doses where cellular responses often appear to deviate from the linear, no-threshold hypothesis. At low doses, effects may also be dependent on cellular conditions as opposed to dose. The cellular and molecular carcinogenic effects of radon exposure have been observed to be both numerous and complex and the elevated chronic exposure of man may therefore pose a significant public health risk that may extend beyond the association with lung carcinogenesis

ImuB and ImuC contribute to UV-induced mutagenesis as part of the SOS regulon in Pseudomonas aeruginosa

DNA damage-induced mutagenesis is a process governed by the SOS system that requires the activity of specialized DNA polymerases. These polymerases, which are devoid of proof-reading activity, serve to increase the probability of survival under stressful conditions in exchange for an error-prone DNA synthesis. As an opportunistic pathogen of humans, Pseudomonas aeruginosa employs adaptive responses that originally evolved for survival in many diverse and often stressful environmental conditions, where the action of error-prone DNA polymerases may be crucial. In this study, we have investigated the role of the polymerases ImuB and ImuC in P. aeruginosa DNA-damage induced mutagenesis. UV irradiation of imuB- and imuC-deletion mutants showed that both genes contribute to UV-induced mutagenesis in this bacterium. Furthermore, we confirmed that UV treatment significantly increase the expression levels of the imuB and imuC genes and that they are co-transcribed as a single transcriptional unit under the control of LexA as part of the SOS regulon in P. aeruginosa. Environ. Mol. Mutagen. 2019. © 2019 Wiley Periodicals, Inc.Fil: Lujan, Adela Maria. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Investigaciones en Química Biológica de Córdoba; Argentina. Universidad Católica de Córdoba. Instituto de Investigaciones en Recursos Naturales y Sustentabilidad José Sanchez Labrador S. J. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Recursos Naturales y Sustentabilidad José Sanchez Labrador S. J.; ArgentinaFil: Moyano, Alejandro Jose. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Investigaciones en Química Biológica de Córdoba; ArgentinaFil: Martino, Román Alejandro. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Investigaciones en Química Biológica de Córdoba; ArgentinaFil: Feliziani, Sofía. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Investigaciones en Química Biológica de Córdoba; ArgentinaFil: Urretavizcaya, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Investigaciones en Química Biológica de Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Biológica; ArgentinaFil: Smania, Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Investigaciones en Química Biológica de Córdoba; Argentin

Genotoxic responses at low doses for chemicals requiring metabolic activation using different human cell lines.

ro-carcinogens e.g. B[a]P and PhIP require metabolic activation to exert genotoxicity. Both B[a]P and PhIP are known to cause different types of cancers, however, very little is known about the dose response of these two chemicals at low concentrations. This study was conducted to determine the effect of low doses of B[a]P and PhIP and their exposure time on cell lines with varying levels of metabolic activity.Micronucleus and HPRT assays were conducted to determine the effect of low doses of B[a]P on micronuclei induction and mutation frequency following 4 or 24 h exposure. MCL-5 and HepG2 cell lines showed higher induction of micronuclei irrespective of B[a]P dose and exposure time. Micronuclei induction was least in AHH-1 while TK-6 cells showed no micronuclei induction. HPRT assay also showed higher mutation frequency in MCL-5 as compared to AHH-1 at both time exposures. Analysis of mutation spectra of MCL-5 and AHH-1 HPRT mutants revealed that the type of mutations observed in B[a]P treated cells were different to those observed in untreated control B[a]P-induced mutations were predominantly G ->T transversions. Real time PCR assays revealed higher induction of CYP1A1 and CY1A2 enzymes in response to B[a]P in MCL-5 and HepG2 cell lines.Studies on PhIP showed significantly higher cytotoxicity, genotoxicity and mutation frequency in the MCL-5 and HepG2 cell lines than AHH-1 cells. Micronucleus assays (24h) revealed 1.56 and 1.9-.fold increase in micronuclei induction in MCL-5 and HepG2, respectively as compared to control. A similar trend was observed in 4h PhIP exposure study, where MCL-5 and HepG2 had 1.83 and 1.92-.fold increase respectively. These findings are in line with the metabolic potential of the cell lines. Real-time PCR assays showed that over all, expression of CYP1A1 and CY1A2 was higher in HepG2 than MCL-5 following PhIP exposure for 24h. PhIP was observed to induce a significantly higher mutation frequency in MCL-5 cell lines than untreated control. Mutation type also varied among PhIP treated and untreated control of MCL-5. PhIP treated MCL-5 cells showed predominantly G ->T transversions.These studies showed that cells with higher metabolic activity are relatively more capable of activating B[a]P and PhIP and therefore show higher genotoxicity in response to dose and exposure of these pro-carcinogens. Considering the results of this study, potential risk of B[a]P and PhIP induced cancers has been discusse

The Cell Cycle & Circadian Clock: a tale of two cycles

Most organisms have evolved an internal timekeeper to anticipate and coordinate internal processes with the external 24-h environment imposed upon all living creatures due to rotation of the Earth around its axis. At the cellular level, the circadian clock is generated by a genetic program in which genes and their protein products generate a molecular oscillator. In mammal cells, this oscillator consists of one essential negative transcription/translation feedback loop and several other positive and negative feedback loops that function mainly to confer robustness and precision to the core negative feedback loop. The work described in Chapter 2 shows that exposure of mice to a mutagenic compound at different times-of-day did not result in differences in mutation frequency. Chapter 3 shows that mice lacking the Cry1 gene or the Cry2 gene have circadian gene expression programs in peripheral tissues like liver and kidney that are out of phase with their behavior. Despite this internal dissonance, the mice did not have decreased survival curves. Chapter 4 shows that even though the Cry genes control cell cycle progression, they do so regardless of an intact circadian clock. Furthermore, this chapter provides evidence that the circadian clock does not control cell cycle progression under normal conditions and after exposure to genotoxic stress in a cell-autonomous manner. Conversely, Chpater 5 shows that genotoxic stress exposure does affect the circadian clock in cells and in mice in an ATM-dependent manner. Chapter 6 shows that microRNAs control the circadian clock by posttranscriptionally controlling expression of clock genes

A clamp ligation method for point mutational spectrometry : marked increase in scanning range for the human genome

Thesis (Ph. D.)--Massachusetts Institute of Technology, Division of Bioengineering and Environmental Health, 2002.Includes bibliographical references (leaves 176-200).The study of human mutagenesis requires methods of measuring somatic mutations in normal human tissues and inherited mutations in human populations. Such methods should permit measurement of rare mutations in the presence of abundant wild-type copies and should be general to the human genome. A sensitivity of 2 x 10-6 for point mutations was recently achieved in human cells using a novel method of target isolation, constant denaturant capillary electrophoresis (CDCE), and high-fidelity polymerase chain reaction (hifi-PCR) (Li-Sucholeiki and Thilly, 2000). This method is applicable to 100-base pair (bp) DNA domains juxtaposed with a naturally occurring domain of a higher melting temperature, or a natural clamp. Such sequence domains represent about 9% of the human genome. To permit analysis of rare point mutations in the human genome more generally, this thesis developed a procedure in which a clamp can be ligated to any 100-bp sequence of interest. This procedure was combined with the previous method to create a new method of point mutational analysis that is not dependent on a naturally occurring clamp. To demonstrate the new method, a sequence with a natural clamp, a part of the human hypoxanthine-guanine phosphoribosyl transferase (HPRT) gene (cDNA-bp 223-318), was analyzed using both the natural and ligated clamps. A sensitivity of 2 x 10-5 in human cells was demonstrated using the ligated clamp as opposed to 5 x 10-6 using the natural clamp.(cont.) The sensitivity of the new method using the ligated clamp was demonstrated to be limited by the fidelity of Pfu DNA polymerase used for PCR. The sequence of the ligated clamp accounted for the differences in sensitivity as a result of causing a decreased efficiency of mutant enrichment by CDCE. The new method can be applied to measure somatic mutations in normal human tissues, such as lung tissues, in which point mutations at fractions above 10-5 have been observed. This method can also detect predominant inherited mutations even for genes carrying recessive deleterious alleles in pooled samples derived from a large number of individuals.by Andrea Seungsun Kim.Ph.D

Impact of the human intestinal microbiota on the metabolism and toxic properties of the meat contaminant 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine

Cancer is a major disease burden worldwide that accounts in countries with a Western lifestyle for 20% of the mortality rate. Epidemiological evidence suggests that diet makes a substantial contribution to the burden of human cancer. It is the consumption of meat, and in particular red meat, that has shown the strongest association with human neoplastic disease, particularly tumors of the colon and rectum. Cooking of meat is known to generate a family of promutagenic/procarcinogenic compounds, including the heterocyclic aromatic amine class of chemical compounds. Of the 19 heterocyclic amines identified so far, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is frequently the most mass abundant heterocyclic amine produced during the cooking of beef, pork and chicken. The human intake of PhIP varies with food type and cooking conditions and is estimated to range from nanograms to tens of micrograms per day, depending on individual dietary and cooking preferences. Assessment studies based on rodent tumor data and the abundance of PhIP in the diet have indicated that this heterocyclic amine may be a risk factor in human colon, breast and prostate carcinogenesis; which co-incidentally are the three most common sites of diet-associated cancer in the Western world. As a means of determining the potential health risks associated with heterocyclic amines, several dietary studies have been conducted on the metabolism and disposition of these compounds in humans. So far, most investigations focused on the activation and detoxification of heterocyclic amines by mammalian phase I and II enzymes. In common with other aromatic amines, PhIP is metabolically activated by N-oxidation of the exocyclic amino group, a reaction mediated mainly by the cytochrome P450 isoenzyme CYP1A2. On the other hand, the involvement of the intestinal microbiota in the digestive fate of heterocyclic amines remains poorly investigated. Recent research has however shown that the amount of PhIP metabolites excreted in the urine of humans following ingestion of PhIP in a meat matrix is significantly lower than that of patients administered PhIP in a capsule. This indicates that PhIP provided in capsule form is more bioavailable than PhIP ingested from meat. The non-bioavailable fraction reaches the colon and becomes available for biotransformation by the colonic bacteria. At the start of this research only a few, partly conflicting results from studies with lactobacilli and intestinal microorganisms were available. Indications exist that the intestinal microbiota are essential to the induction of DNA damage by PhIP in HFA rats. Information on the bacterial metabolism of native heterocyclic amines is however scarce and limited to some studies on the quinoline type heterocyclic amines. Therefore, the main objective of this work was to explore the possible role of the human intestinal microbiota in the metabolism and biological activity of PhIP. To do this, an integrated in vitro-in vivo approach was followed, combining fecal incubations, human studies and mammalian cell lines. In the first part of this research, the microbial metabolism of PhIP was investigated. A preliminar explorative study in which PhIP was anaerobically incubated with stools freshly collected from six healthy volunteers demonstrated that PhIP was extensively transformed by the human intestinal bacteria. HPLC analysis revealed that the human fecal microbiota converted PhIP specifically into one major derivative. ESI-MS/MS, HRMS, 1D (1H, 13C, DEPT) and 2D (gCOSY, gTOCSY, gHMBC, gHSQC) NMR and IC analysis elucidated the complete chemical identity of the microbial PhIP metabolite, as 7-hydroxy-5-methyl-3-phenyl-6,7,8,9-tetrahydropyrido[3,2:4,5]imidazo[1,2-a]pyrimidin-5-ium chloride (PhIP-M1). To evaluate whether this newly identified microbial PhIP metabolite could be produced by the intestinal bacteria in vivo as well, a human intervention trial was set up. Six human subjects were fed 150 g of cooked chicken containing 0.88-4.7 µg PhIP, and urine and feces collections were obtained during 72 h after the meal. PhIP-M1 and its trideuterated derivate were synthesized and a rapid and accurate solid-phase extraction LC-ESI-MS/MS method for the simultaneous quantification of PhIP and PhIP-M1 in human urine and feces was developed. Of the ingested PhIP dose, volunteers excreted 12-21% as PhIP and 1.2-15% as PhIP-M1 in urine, and 26-42% as PhIP and 0.9-11% as PhIP-M1 in feces. The rate of PhIP-M1 excretion varied among the subjects. Yet, an increase in urinary excretion was observed for successive time increments, whereas for PhIP the majority was excreted in the first 24 h. These findings confirmed that the human intestinal bacteria significantly contribute to the overall metabolism and disposition of PhIP in vivo. After the observation that PhIP could be metabolically converted by the human intestinal bacteria in vitro and in vivo, the next step was to identify and characterize the bacterial species responsible for this process. Two PhIP transforming strains PhIP-M1-a and PhIP-M1-b were isolated from human feces and identified by a combination of microscopy, PCR-DGGE, FAFLPTM and pheS sequence analyses as Enterococcus faecium. Some strains from culture collections belonging to the species Enterococcus durans, Enterococcus avium, Enterococcus faecium and Lactobacillus reuteri were also able to perform this transformation. Glycerol was identified as a fecal matrix constituent required for PhIP conversion. Abiotic synthesis of PhIP-M1 and quantification of the glycerol metabolite 3-hydroxypropopionaldehyde (3-HPA) confirmed that the anaerobic fermentation of glycerol via 3-HPA is the critical bacterial transformation process responsible for the formation of PhIP-M1. Although several lactobacilli, as well as other bacterial species have been shown to use glycerol as an external electron acceptor, we are the first to relate bacterial species of the genus Enterococcus to this anaerobic pathway of glycerol dissimilation. In addition, we have shown that PhIP-M1 production occurs under proteolytic conditions. This was true for mixed fecal microbiota as well as for the Enterococcus faecium PhIP-M1-a transforming strain. The production of PhIP-M1 was shown to be dependent on interindividual differences. A first explorative experiment with six human fecal samples demonstrated this factor. Subsequent fecal incubations with eighteen human microbiota confirmed that individuals could be separated into low, moderate and high PhIP-M1 producers with transformation efficiencies ranging from 1.8 to 96%. Finally, significant differences in intestinal PhIP-M1 production were found to determine differences in urinary and fecal PhIP-M1 excretion in vivo in humans. This indicated that interindividual differences in microbial composition and metabolism may at least be equally important than differential expression and genetic polymorphisms in phase I and II endogenous enzymes, which have been considered so far as the obvious candidates responsible for individual variability in PhIP metabolism, bioavailability and carcinogenicity. In the second part of this doctoral research, the impact of the intestinal microbiota on the biological activity of PhIP was evaluated. Since ligation of the biliary duct has been shown not to alter the genotoxic potential of PhIP, the deconjugation of reactive glucuronides by bacterial β-glucuronidase is most likely not to alter the metabolic fate and bioactivity of PhIP. Therefore, it was very much conceivable that the microbial formation of PhIP-M1 contributed to the final genotoxic and carcinogenic activity of PhIP. Firstly, it was observed that PhIP-M1, as analyzed using the Salmonella typhimurium strains TA98, TA100 and TA102, yielded no significant mutagenic response. Subsequently, it was assessed whether PhIP-M1 could exert any cytotoxic or genotoxic effects towards a human intestinal cell line. PhIP-M1 was shown to induce DNA damage, cell cycle arrest, apoptosis and eventually cell death and growth inhibition towards the epithelial Caco-2 cell line. DNA damage in Caco-2 cells was detected using the Comet assay. This assay is recognized as a sensitive tool widely used for the evaluation of primary DNA damages at the individual cell level, while the bacterial Ames assay only detects mutagenic effects if the DNA damage induced remained after cell division. The conversion of PhIP into PhIP-M1 was therefore considered as a microbial bioactivation. As the genomic and cellular events of CYP1A2-activated PhIP in different in vitro cell systems are not significantly higher than those observed for PhIP-M1 in our test system, the physiological relevance of this newly identified microbial PhIP derivate in PhIP carcinogenicity may not be neglected. Finally, it was investigated whether addition of native chicory inulin could inhibit the extent of microbial PhIP bioactivation. Inulin is generally considered to exert prebiotic effects as it stimulates health-promoting bacteria in the human gut such as bifidobacteria. However, it is also hypothesized that it may exert chemopreventive effects by the indirect suppression of microbial groups such as enterococci that are responsible for the hazardous conversion of carcinogenic compounds such as PhIP. In addition, inulin is known to bring about prebiotic effects at the level of the metabolic activity, resulting in a saccharolytic fermentation pattern and acidic environment. Supplementation of inulin during several weeks to a full-scale SHIME reactor showed significant inhibitory effects towards PhIP bioactivation, in particular in the transverse colon compartment. Interestingly, the strongest decrease in proteolytic end products was also observed in this region of the colon, indicating an indirect relationship with the chemopreventive effects from inulin. As the typical proteolytic conditions in the distal parts of the colon are normally more detrimental to the host in vivo, in particular in the light of the microbial PhIP bioactivation process, these positive modifications in the metabolism and microbial community indicate that inulin is a promising chemopreventive agent