Abyssal fauna, benthic microbes, and organic matter quality across a range of trophic conditions in the western Pacific ocean

Abstract The abyssal plain covers more than half the Earth's surface. The main food source to abyssal ecosystems is phytodetritus, which originates from phytoplankton in the surface ocean, and thus its variability to the seafloor is a major driver of abyssal ecosystem biomass and functioning. In this study, we conducted a comparative survey on organic matter (OM) quality and quantity in abyssal plain sediments and examined the distributions of megafauna, macrofauna, meiofauna, prokaryotes, and viruses in eutrophic (39°N), oligotrophic (1°N), and ultra-oligotrophic (12°N) areas of the western Pacific. We also analyzed stable carbon and nitrogen isotopic compositions of organisms at 39°N and 1°N to assess differences in benthic abyssal food-web structures with contrasting trophic states. Sediments collected at 39°N presented highest concentrations of total organic carbon (TOC) and labile OM, and high diffusive oxygen uptake rates. By contrast, the lowest values were found at 12°N. Vertical distributions of sediment macrofauna, meiofauna, and prokaryotes matched with labile OM profiles. There were prominent differences in abundances of macro- and megafauna among stations with different OM fluxes, whereas the abundance of meiofauna and prokaryotes showed smaller differences among stations. Such differences could be explained by higher turnover rates of smaller organisms. Food-web structures of abyssal plains are likely influenced by both the type and size of primary producers in surface ocean. Our results underscore the crucial importance of OM fluxes and their compositions to the abundances and vertical profiles of labile OM and benthic biota in abyssal ecosystems

Genome wide screen identifies microsatellite markers associated with acute adverse effects following radiotherapy in cancer patients

<p>Abstract</p> <p>Background</p> <p>The response of normal tissues in cancer patients undergoing radiotherapy varies, possibly due to genetic differences underlying variation in radiosensitivity.</p> <p>Methods</p> <p>Cancer patients (n = 360) were selected retrospectively from the RadGenomics project. Adverse effects within 3 months of radiotherapy completion were graded using the National Cancer Institute Common Toxicity Criteria; high grade group were grade 3 or more (n = 180), low grade group were grade 1 or less (n = 180). Pooled genomic DNA (gDNA) (n = 90 from each group) was screened using 23,244 microsatellites. Markers with different inter-group frequencies (Fisher exact test <it>P </it>< 0.05) were analyzed using the remaining pooled gDNA. Silencing RNA treatment was performed in cultured normal human skin fibroblasts.</p> <p>Results</p> <p>Forty-seven markers had positive association values; including one in the <it>SEMA3A </it>promoter region (P = 1.24 × 10^-5). <it>SEMA3A </it>knockdown enhanced radiation resistance.</p> <p>Conclusions</p> <p>This study identified 47 putative radiosensitivity markers, and suggested a role for <it>SEMA3A </it>in radiosensitivity.</p

Influence of multiple genetic polymorphisms on early adverse reaction in the gastrointestinal tract of patients with cervical cancer treated with pelvic radiation therapy

[Objectives] Cancer patients experience individual variation in normal tissue reactions after radiotherapy (RT). Such reactions to RT are quite complex, with multiple genetic factors contributing to a patient\u27 s susceptibility for the reactions to RT. A risk of intestinal toxicity could be related to individual differences in radiosensitivities of the mitogenic crypt cells. We hypothesized that gene variation likely to affect cell-cycle regulation could contribute to heterogeneity in the risk of adverse intestinal reactions in CC patients undergoing RT.[Methods] We examined 208 cervical cancer patients who have treated with pelvic radiotherapy as eligible for the genetic investigation. An early gastrointestinal reaction was graded using the NCICTC. The subjects were dichotomized into a lower-grade group (n = 150) and a higher-grade group (n = 58). Genomic DNA was genotyped, and association with the risk of adverse reaction for 49 functional SNPs of 22 candidate gens was assessed by single-locus, haplotype, and multilocus analysis.[Results] Our analysis revealed two haplotypes of NPAT-ATM and AURKA and two single loci of PSMB8 and CASP7 contribute to the risk of adverse intestinal reaction after RT. Patients who had two or more of the risk genotype of these four genes showed higher risk than other patients.[Conclusions] Genetic variations in the genes functioned on cell-cycle regulation may contribute to individual radiosensitivity of intestine. Identification of the novel risk genotypes would improve our understanding into the contribution of genetic factors to individual radiosensitivity and could be used to stratify the genetic risk in CC patients.The 2nd Japan-China Symposium on Cancer Researc

Association of the caspase-7 Asp4Glu polymorphism with increased risk of adverse reaction in the gastrointestinal tract after pelvic radiotherapy in cervical cancer patients

Caspase-7 (CASP7) is one of the effector caspases responsible for cleaving intracellular substrates involved in promoting the apoptotic phenotype. Interestingly a role for CASP7 in cell cycle progression at mitosis has also been suggested. Additionally, CASP7 polymorphisms are associated with increased risk for several types of cancer such as breast cancer, endometrial cancer and lung cancer. However little is known about the association of CASP7 with individual radiosensitivity. Therefore, in this study, we analyzed the association of functional polymorphisms in CASP7 with the risk of an adverse reaction in the intestinal tract after radiotherapy.A total of 208 cervical cancer patients who had been treated with pelvic radiotherapy were genetically analyzed. Early gastrointestinal reactions were graded using the National Cancer Institute Common Toxicity Criteria, and patients were dichotomized into a lower-grade (LG) group (! Grade = 0 or 1, n = 150) and a higher-grade (HG) group (Grade = 2 or 3, n = 58). Three SNPs with minor allele frequencies of more than 5% in our healthy control samples, rs12415607 (C-1222A), rs11593766 (T398G, Asp4Glu), and rs2227310 (C1151G, Asp255Glu), were subjected to genotype and haplotype analyses in the cervical cancer patients.Among these 3 SNPs, only rs11593766 was found to be associated with a risk of adverse reaction in the intestinal tract. The frequency of the G allele of this SNP was significantly higher in the HG group (18%) than in the LG group (9%; odds ratio [OR], 2.24; 95% confidence interval [CI], 1.18-4.21; P = 0.016). The GG and TG genotypes of rs11593766 were significantly associated with an increased risk of adverse reaction in the intestinal tract (OR, 2.15; 95% CI, 1.04-4.44; P = 0.038). No significant haplotype including rs11593766 was detected. Diplotypes of NPAT-ATM and AURKA have also been reported to con t! ribute to the risk of adverse intestinal reaction after radiotherapy, and we found that patients who had two or more of the NPAT-ATM, AURKA or CASP7 risk genotypes showed higher risk than other patients (OR, 3.60; 95% CI, 1.83-7.19; P = 0.00007).Our results suggest that the rs11593766 GG and TG genotypes (Glu/Glu or Asp/Glu) of CASP7 might contribute to the individual risk of adverse intestinal reaction after radiotherapy.14th International Congress of Radiation Research(ICRR’2011

Direct determination of the radiosensitivity-associated haplotype in CD44 gene by igMDA method using frozen human blood samples

Purpose: A haplotype GGTT of four SNPs (rs187116, rs3794116, rs3794107, rs8193) that spans 80 kb distance in CD44 gene has been reported by statistical association analysis to show significant greater early adverse skin reaction risk (odds ratio = 2.17; 95% confidence interval, 1.07&#8211;4.43) after radiotherapy of Japanese breast cancer patients (Suga et al. Int J Radiat Oncol Biol Phys. 2007, 69, 685-693). For future individualized clinical applications, we developed the igMDA (in-gel multiple displacement amplification) method (Michikawa et al. Anal Biochem. 2008, 383, 151-158) and improved to be capable to use frozen human blood samples, instead of the frozen EB virus-transformed human B lymphoblastoid cells of the original method. In this study, we applied the improved protocol for direct determination of the individuals diplotype in CD44 gene. \nMaterials and Methods: Frozen blood samples from breast cancer patients who registered from 2001 to 2005 for RadGenomics Project were used in this study. All the patients provided written informed consent to participate in the study, which was approved by the Ethical Committee at NIRS and by each collaborating institution. The frozen blood samples were thawed at room temperature and centrifuged at 3,000 x g for 5 min to remove liquid component of bloods. Blood cells were then washed by PBS once and number of cells with nuclear DNA was microscopically counted by staining their nuclear DNA with PicoGreen. The cellular DNA-embedded agarose gel solution was first solidified at room temperature then small pieces (approximately 1 micro liter) were picked to aliquot, instead of directly aliquoting the embedded agarose gel solution before solidification in the original conditions. The multiple displacement amplification reaction that uses Phi29 DNA polymerase to comprehensively amplify limited amount of DNA embedded in the aliquoted agarose gel pieces was used with the original conditions. Post-amplification screening of CD44 gene containing-amplicons was carried out using a PCR primer set designed to avoid the copy number variation region shown in the database of this gene. Genotyping of the four tag SNPs were carried out by the allele-specific real-time quantitative PCR. \nResults: Number of nuclear DNA-positive cells and volume of the cell suspension to be embedded into agarose gel solution were carefully titrated to make an appropriately diluted condition to isolate sufficient number of single homologous chromosomes. Resulting conditions provided average 23.2 (SD+-9.2) positive amplicons in a set of 94 amplicons (n=40). Full length coverage ratio of the positive amplicons was average 15.8 % (SD+-8.7). Overall successful haplotype determination rate was 80%. \nConclusions: Frozen human blood samples can be used for direct determination of radiosensitivity-associated haplotype of CD44 gene by the improved igMDA method.Biotecnologia Habana 2009, Medical Applications of Biotechnolog

Association of polymorphisms in hyaluronan receptor CD44 with radiotherapy effectiveness in patients with cervical cancer

Purpose: Hyaluronan (HA), a polysaccharide, is synthesized by a hyaluronan synthase (HAS). HA interacts with cells in dynamic processes such as embryogenesis and oncogenesis through interactions with several types of surface receptors like CD44 that play a role in regulating important signaling pathways, including the PI3K pathway. To identify predictive markers for radiotherapy effectiveness in cervical cancer, we have been analyzing the expression and genetic variation of some key genes such as FGF2, CD44, and HAS1. This study sought to determine the association between polymorphisms in CD44 and HAS1 genes with radiotherapy effectiveness in patients with cervical cancer.Materials and Methods: The study population comprised 121 cervical cancer patients who were treated with pelvic radiotherapy (the median dose of external beam = 50.6 Gy [range, 45.0 - 60.6 Gy] and median dose of brachytherapy = 24.0 Gy [range, 19.0 - 36.5 Gy]). The patients were defined as good (n = 82, mean age = 61 years [range, 32-83 years]) or poor (n = 39, mean age = 54 years [36-82 years]) responders on the basis of their 2-year disease-free survival. Genomic DNA was obtained from their blood samples and was genotyped using 19 SNPs in CD44 and 4 SNPs in HAS1. The association between each SNP and prognosis was evaluated by multivariate logistic regression analysis conditioned on the data pertaining to smoking, histological classification (squamous cell carcinoma/adenocarcinoma), and the International Federation of Gynecology and Obstetrics (FIGO) staging (I, II, III, IVA) of the tumors.Results: In logistic regression analysis conditioned on FIGO staging and smoking habits (the other factors did not contribute to the final model), P-values of 0.0056 was obtained for the SNP, T-2016C in CD44 (OR = 2.49, 95% CI = 1.31 - 4.76). The variant was located in the 5\u27 upstream region of the gene, suggesting that patients with the variant contribute to produce different amounts of CD44. Conclusions: Thus, radiotherapy effectiveness in patients with cervical cancer may be predicted, at least in part, by the genotype of CD44. Because of the limited sample size used in this study, further replication studies and functional analyses are required to confirm the results of the association analysis. However, the present data may be useful for analyzing the mechanisms underlying interaction between HA and CD44 and the subsequent cervical cancer-associated signaling.CSH Asia / ICMS (The International Cancer Microenvironment Society) Joint Conference on Tumor Microenvironmen

Screening of radiation susceptibility genes by single-nucleotide polymorphisms and haplotype analysis

Radiotherapy for breast cancer patients occasionally induces adverse effects. The adverse reactions to radiotherapy are caused by multiple factors, including individual genetic differences. The heterogeneity in normal tissue reactions may result from the combined effect of several different genetic alterations. Single nucleotide polymorphisms (SNPs) and derived haplotypes within multiple genes may be used to detect the genetic alterations related to the heterogeneity in normal tissue reactions. DNA was sampled from 397 Japanese breast cancer patients who qualified for breast-conserving radiotherapy. Using the NCI-CTC scoring system version 2, the patients were grouped according to adverse skin reactions at 3 months of starting radiotherapy (grade = 0, n = 230; grade &#8805; 1, n = 167). Nine hundred and ninety-nine SNPs from 137 candidate genes for radiation susceptibility were genotyped, and haplotype associations between groups were assessed. Global haplotype association analysis (P < 0.05 and FDR < 0.005) indicated that estimated haplotypes in three loci were associated with the risk of adverse skin reactions. Comparison of risk haplotype to the most frequent haplotype in each locus showed haplotype CGATA(OR = 2.04; 95% CI, 1.19-3.52) and TGATG(OR = 5.05; 95% CI, 1.31-19.53) and TGAGG(OR = 12.89; 95% CI, 1.53-108.25) in TGFBI , CT in IL1A (OR = 1.83; 95% CI, 1.17-2.85), and AGT in GSTA4 (OR = 2.77; 95% CI, 1.23-6.22) had significantly greater adverse skin reactions risk.In conclusion, Individual radiosensitivity may be partly determined by combinations of these haplotypes in multiple loci. This would provide an understanding of the mechanisms underlying the genetic variation in radiation sensitivity or resistance among the population, and would show the possibility of prediction of the risk of adverse skin reactions prior to radiation therapy.10th Anniversary of Kazusa Arc International Symposium on Advanced Functional Genomic

Variants Of Cell-Cycle Regulatory Genes Are Associated With The Risk Of An Early Adverse Reaction After Radiotherapy For Cervical Cancer

Cancer patients exhibit individual variability in their normal tissue reactions after radiation therapy (RT). The observed adverse reactions to RT are quiet complex and individual genetic factors may contribute in part to causing such reactions. Cervical cancer is the second most common malignancy among women worldwide and the currently preferred therapeutic modality for cervical cancer is concomitant chemotherapy and radiotherapy. Little is known about the genetic factors capable of generating biological outcomes that are associated with adverse reactions to RT in cervical cancer patients.Treatment of cervical cancer with RT can result in other tissues with a high radiosensitivity being exposed to the radiation field. In particular, the intestines show significant radiation sensitivity and contain highly proliferative cryptic cells. Previously, we have shown that variants of cell-cycle regulatory genes are associated with the risk of an early adverse skin reaction, which may damage the self-renewing cells of the epidermis.In this study, we analyzed the association of single nucleotide polymorphisms (SNPs) in 13 cell-cycle regulatory or related genes with the risk of adverse intestinal reactions after RT. DNA was sampled from 208 cervical cancer patients who qualified for RT. SNP typing was performed using the MassARRAY system (Sequenom, CA) according to the manufacturer\u27s instructions. Each SNP in genes such as /TP53/ and /AURKA/ was associated with the risk of adverse reaction. We conclude that that the radiosensitivity of an individual cervical cancer patient can be determined by polymorphisms in multiple loci. Furthermore, our findings may lead to a better understanding of the mechanisms underlying the genetic variation in either radiation sensitivity or resistance among cancer patients.Biotecnologia Habana 2009, Medical Applications of Biotechnolog