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There are unexplained geographical variations in the incidence of kidney cancer with the high rates reported in Baltic countries, as well as eastern and central Europe. Having access to a large and well-annotated collection of “tumor/non-tumor” pairs of kidney cancer patients from the Czech Republic, Romania, Serbia, UK, and Russia, we aimed to analyze the morphology of non-neoplastic renal tissue in nephrectomy specimens. By applying digital pathology, we performed a microscopic examination of 1012 frozen non-neoplastic kidney tissues from patients with renal cell carcinoma. Four components of renal parenchyma were evaluated and scored for the intensity of interstitial inflammation and fibrosis, tubular atrophy, glomerulosclerosis, and arterial wall thickening, globally called chronic renal parenchymal changes. Moderate or severe changes were observed in 54 (5.3%) of patients with predominance of occurrence in Romania (OR = 2.67, CI 1.07–6.67) and Serbia (OR = 4.37, CI 1.20–15.96) in reference to those from Russia. Further adjustment for comorbidities, tumor characteristics, and stage did not change risk estimates. In multinomial regression model, relative probability of non-glomerular changes was 5.22 times higher for Romania and Serbia compared to Russia. Our findings show that the frequency of chronic renal parenchymal changes, with the predominance of chronic interstitial nephritis pattern, in kidney cancer patients varies by country, significantly more frequent in countries located in central and southeastern Europe where the incidence of kidney cancer has been reported to be moderate to high. The observed association between these pathological features and living in certain geographic areas requires a larger population-based study to confirm this association on a large scale. Supplementary Information The online version contains supplementary material available at 10.1007/s00428-020-02986-3.

Background There are unexplained geographical variations in the incidence of kidney cancer with the high rates reported in Baltic countries, as well as eastern and central Europe. Analysis of non-neoplastic tissues is a way to better understand the carcinogenesis. Methods Having access to a rich, well-annotated collection of “tumor/non-tumor” pairs of kidney cancer patients from Czech Republic, Romania, Serbia, United Kingdom, and Russia for studying genomics of kidney cancer, we aimed to analyze morphology of non-neoplastic renal tissue. By applying digital pathology, we performed microscopic examination of 1012 frozen non-neoplastic kidney tissues from patients with renal cell carcinoma. Renal parenchyma was evaluated and scored for the interstitial inflammation and fibrosis, tubular atrophy, glomerulosclerosis and arterial wall thickening, globally called chronic renal parenchymal changes. Results Moderate or severe changes was observed in 54 (5.3%) of patients with predominance of occurrence in Romania (OR = 2.67, CI 1.07–6.67) and Serbia (OR = 4.37, CI 1.20-15.96) in reference to those from Russia. Further adjustment for comorbidities, tumor characterstics and stage did not change risk estimates. In multinomial regression model, relative probability of non-glomerular changes were 5.22 times higher for Romania and Serbia compered to Russia. Conclusion Our findings show that the frequency of chronic renal parenchymal changes in kidney cancer patients varies by country, significantly more frequent in countries located in central and southeastern Europe where the incidence of kidney cancer has been reported to be high. We suggest that these parenchymal changes, possibly linked to environmental exposures, may be relevant to renal carcinogenesis in these countries.

Promoter hypermethylation of tumor suppressor genes presents promising markers for lung cancer diagnosis and prognosis. The purpose of this study was to determine the association between the promoter hypermethylation of multiple genes and 5-year survival rate in patients with Non-small cell lung cancer (NSCLC).Primary tumor samples (n = 65), corresponding nonmalignant lung tissues (n = 65), and circulating blood were obtained from NSCLC patients who underwent curative surgery. Promoter methylation status in seven genes (RASSF1A, CDH13, MGMT, ESR1, DAPK, SOX1, and HOXA9) was quantified by using bisulfite pyrosequencing. Five-year survival data were obtained by a clinician. Cox proportional hazards models were used to analyze the associations between gene methylation status and overall patient survival.The 5-year survival of the patients with SOX1 aberrant tumor methylation was found to be statistically significantly shorter than for those patients without aberrant tumor methylation (P = 0.01). This effect was independent of TNM stage. No significant survival differences were associated with aberrant methylation in other genes tested in either of the two tissue types.Our study shows that SOX1 promoter hypermethylation in NSCLC tumors is significantly associated with inferior survival, showing promise as a useful prognostic biomarker in patients with NSCLC.

Acute renal failure (ARF) represents a severe complication of malignancies, that causes significant morbidity and mortality. ARF is a common part of multiple organ dysfunction in critically ill patients with cancer with reported mortality rates from 72% to 85% in patients who need renal replacement therapy. The pathways leading to ARF in cancer patients are common to the development of ARF in other conditions. However, certain factors leading to the development of ARF may be associated to the tumor or to the tumor therapy. The purpose of this review is to give specific aspects of renal disease in critically ill cancer patients (CICPs), to overview the causes of ARF in CICPs and to describe recent progress in the management of these complications, including treatment toxicity and bone marrow transplantation (BMT). The prevention of ARF is obligatory and therefore the possible treatments of ARF in CICPs are also discussed.

The development of cancer is driven by the accumulation of many oncogenesis-related genetic alterations and tumorigenesis is triggered by complex networks of involved genes rather than independent actions. To explore the epistasis existing among oncogenesis-related genes in lung cancer development, we conducted pairwise genetic interaction analyses among 35,031 SNPs from 2027 oncogenesis-related genes. The genotypes from three independent genome-wide association studies including a total of 24,037 lung cancer patients and 20,401 healthy controls with Caucasian ancestry were analyzed in the study. Using a two-stage study design including discovery and replication studies, and stringent Bonferroni correction for multiple statistical analysis, we identified significant genetic interactions between SNPs in RGL1:RAD51B (OR=0.44, p value=3.27x10-11 in overall lung cancer and OR=0.41, p value=9.71x10-11 in non-small cell lung cancer), SYNE1:RNF43 (OR=0.73, p value=1.01x10-12 in adenocarcinoma) and FHIT:TSPAN8 (OR=1.82, p value=7.62x10-11 in squamous cell carcinoma) in our analysis. None of these genes have been identified from previous main effect association studies in lung cancer. Further eQTL gene expression analysis in lung tissues provided information supporting the functional role of the identified epistasis in lung tumorigenesis. Gene set enrichment analysis revealed potential pathways and gene networks underlying molecular mechanisms in overall lung cancer as well as histology subtypes development. Our results provide evidence that genetic interactions between oncogenesis-related genes play an important role in lung tumorigenesis and epistasis analysis, combined with functional annotation, provides a valuable tool for uncovering functional novel susceptibility genes that contribute to lung cancer development by interacting with other modifier genes.

Non-small cell lung cancer is the most common type of lung cancer. Both environmental and genetic risk factors contribute to lung carcinogenesis. We conducted a genome-wide interaction analysis between single nucleotide polymorphisms (SNPs) and smoking status (never-versus ever-smokers) in a European-descent population. We adopted a two-step analysis strategy in the discovery stage: we first conducted a case-only interaction analysis to assess the relationship between SNPs and smoking behavior using 13 336 non-small cell lung cancer cases. Candidate SNPs with P-value

Although several lung cancer susceptibility loci have been identified, much of the heritability for lung cancer remains unexplained. Here 14,803 cases and 12,262 controls of European descent were genotyped on the OncoArray and combined with existing data for an aggregated genome-wide association study (GWAS) analysis of lung cancer in 29,266 cases and 56,450 controls. We identified 18 susceptibility loci achieving genome-wide significance, including 10 new loci. The new loci highlight the striking heterogeneity in genetic susceptibility across the histological subtypes of lung cancer, with four loci associated with lung cancer overall and six loci associated with lung adenocarcinoma. Gene expression quantitative trait locus (eQTL) analysis in 1,425 normal lung tissue samples highlights RNASET2, SECISBP2L and NRG1 as candidate genes. Other loci include genes such as a cholinergic nicotinic receptor, CHRNA2, and the telomere-related genes OFBC1 and RTEL1. Further exploration of the target genes will continue to provide new insights into the etiology of lung cancer.

Over 100 single nucleotide polymorphisms (SNP) are validated in the TP53 tumor suppressor gene. They define haplotypes, which may differ in their activities. Therefore, mutation in cancer may occur at different rates depending upon haplotypes. However, these associations may be masked by differences in mutations types and causes of mutagenesis. We have analyzed the associations between 19 SNPs spanning the TP53 locus and a single specific aflatoxin-induced TP53 mutation (R249S) in 85 in hepatocellular carcinoma cases and 132 controls from Thailand. An association with R249S mutation (P = 0.007) was observed for a combination of two SNPs (rs17882227 and rs8064946) in a linkage disequilibrium block extending from upstream of exon 1 to the first half of intron 1. This domain contains two coding sequences overlapping with TP53 (WRAP53 and Hp53int1) suggesting that sequences in TP53 intron 1 encode transcripts that may modulate R249S mutation rate in HCC.

Non-small cell lung cancer (NSCLC) represents 80% of all lung cancers and is the leading cause of cancer death worldwide (1). A number of factors can affect survival, including patient’s age, NSCLC subtype, tumor genetic characteristics, response to therapy. In addition, stage of disease at diagnosis has a profound impact on survival. According to the American Cancer Society, based on analysis of SEER registry data between 1998 and 2000, 5-year survival rates of stage IA and IB are 49% and 45% respectively, however, the rates decrease to around 30% for stage II (A&B), to 14% for IIIA and about 5% for stage IIIB, while stage IV survival rate is merely 1% (2). The vast majority of NSCLC (70%) present as advanced disease.

Sarcoma is the index diagnosis of Li-Fraumeni syndrome (LFS), a familial predisposition to cancer that also includes brain cancer, breast cancer, and adrenal cortical carcinoma. Germline mutations in the TP53 gene are detected in approximately 80% of families that fulfill LFS criteria and in 15% to 25% of families that fulfill criteria for Li-Fraumeni-like syndrome (LFS), a group of related syndromes with broader clinical criteria.The authors of this report used the International Agency for Research on Cancer TP53 database to analyze the types, age at onset and mutation patterns of sarcoma in TP53 mutation carriers. Those data were compared with sarcoma types in the general population of Caucasians using data from the National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) Program.Overall, sarcomas represented 25% of tumors in TP53 mutation carriers, and 95.6% occurred before age 50 years compared with 38.3% before age 50 years in the SEER data set. Sarcomas were more likely to be rhabdomyosarcoma in carriers aged5 years (odds ratio [OR], 11.6; 95% confidence interval [CI], 6.1-21.9) and osteosarcoma in carriers at any age (aged20 years: OR, 1.41; 95% CI, 1.02-1.94; age20 years: OR, 4.61; 95% CI, 2.72-7.83). Early sarcoma (at age20 years) was associated with missense mutations in exons encoding the DNA-binding domain of p53 protein. Conversely, p53 null mutations (frameshift, splice sites, nonsense) and mutations outside the DNA-binding domain were associated with leiomyosarcoma (OR, 10.1; 95% CI, 3.4-29.9), a type of sarcoma that occurred after age 20 years.The current results further demonstrated genotype-phenotype correlations and age-dependent variations in sarcoma types in carriers of germline TP53 mutations.

Background: Little is known about risk factors for childhood rhabdomyosarcoma (RMS) and the histology-specific details are rare. Methods: Case–control studies formed by linking cancer and birth registries of California, Minnesota, New York, Texas and Washington, which included 583 RMS cases (363 embryonal and 85 alveolar RMS) and 57 966 randomly selected control subjects, were analysed using logistic regression. The associations of RMS (overall, and based on embryonal or alveolar histology) with birth weight across five 500 g categories (from 2000 to 4500 g) were examined using normal birth weight (2500–3999 g) as a reference. Large (>90th percentile) and small (

BACKGROUND: Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and adolescents aged

The association between antenatal diagnostic X-ray exposure and risk of rhabdomyosarcoma in children was assessed in a national case-control study of 319 rhabdomyosarcoma cases and 319 matched controls. Data were collected by telephone interviews of subjects' parents. Overall, an odds ratio (OR) of 1.9 [95% confidence interval (CI), 1.1-3.4] was found for any X-ray examination of the mother during pregnancy. Risk was greatest for X-ray exposure during the first trimester (OR, 5.7; 95% CI, 1.2-27.8) and was also increased for the third trimester (OR, 2.0; 95% CI, 0.9-4.6), whereas second trimester exposure was not associated with increased risk. A nonsignificant increase in risk was found for any X-rays of the abdomen, pelvis, chest, or back. Increased risk was significantly associated with “other” X-ray exposures (relative risk, 2.9; 95% CI, 1.1-7.7), primarily composed of dental X-rays. The association was strongest between embryonal rhabdomyosarcoma and first trimester exposure (relative risk, 10.5; 95% CI, 1.5-458.4). This observation regarding embryonal rhabdomyosarcoma, and our previous report of an increased frequency of major malformations in rhabdomyosarcoma are compatible with findings from animal studies in which Ptc heterozygous knockout mice exhibited an increased risk of radiation-induced development defects and of spontaneously occurring embryonal rhabdomyosarcoma. (Cancer Epidemiol Biomarkers Prev 2009;18(4):1271–6)

Acquired pure red-cell aplasia (PRCA) is an uncommon disorder of erythrocytopoiesis that can develop in association with thymic tumors. We present the very rare case of a severely anemic 62-year-old man with PRCA and a concurrent neuroendocrine carcinoid tumor of the thymus. The anterior mediastinal thymus tumor was completely excised, and following histological and immunohistochemical analyses (showing positive staining for cytokeratin, chromogranin A, synaptophysin, and neuron-specific enolase) the diagnosis of a (grade I; T(1)N(0)M(0)) typical carcinoid tumor of the thymus was made. Postoperatively the anemia persisted despite no signs of residual tumor on CT chest. A hematological work up found: normocellularity with

The present analysis investigated the effect of soya foods on serum levels of six inflammatory markers, leptin, adiponectin, monocyte attractant protein 1 (MCP-1), macrophage inflammatory protein-1b (MIP-1b), IL-6 and C-reactive protein (CRP), and their relationship with BMI and lifetime soya intake. We randomised twenty-four men to a high- (two daily servings with 30–35 mg isoflavones per serving) or a low-soya diet for 3 months. After a 1-month washout period, the men crossed over to the other treatment. We used a multiplex bead immunoassay to measure leptin, adiponectin, MCP-1 and MIP-1b and ELISA assays for IL-6 and CRP. The statistical analysis applied mixed models that incorporated the four repeated measurements. The men had a mean age of 58·7 (sd 7·2) years and a mean BMI of 28·4 (sd 4·9) kg/m2. We observed no significant intervention effect of the soya treatment on any of the six markers. After adjustment for age and ethnicity, highly significant associations of BMI and body weight with leptin and MCP-1 emerged. Men with high soya intake early in life also had higher levels of leptin and MCP-1, whereas no association was seen for soya intake during adulthood. MIP-1b, adiponectin, IL-6 and CRP were not related to BMI, body weight or soya intake at any time in life. No intervention effect of soya foods on markers of inflammation was observed in this small study, but adiposity and early-life soya intake were related to higher leptin and MCP-1 levels.

The polymorphic gene NAT2 is a major determinant of N-acetyltransferase activity and, thus, may be responsible for differences in one's ability to bioactivate heterocyclic amines, a class of procarcinogens in cooked meat. An unusually marked geographic variation in enzyme activity has been described for NAT2. The present study re-examines the international direct correlation reported for meat intake and colorectal cancer (CRC) incidence, and evaluates the potential modifying effects of NAT2 phenotype and other lifestyle factors on this correlation. Country-specific CRC incidence data, per capita consumption data for meat and other dietary factors, prevalence of the rapid/intermediate NAT2 phenotype, and prevalence of smoking for 27 countries were used. Multiple linear regression models were fit and partial correlation coefficients (PCCs) were computed for men and women separately. Inclusion of the rapid/intermediate NAT2 phenotype with meat consumption improved the fit of the regression model for CRC incidence in both sexes (males-R (2) = 0.78, compared to 0.70 for meat alone; p for difference in model fit-0.009; females-R (2) = 0.76 compared to 0.69 for meat alone; p = 0.02). Vegetable consumption (inversely and in both sexes) and fish consumption (directly and in men only) were also weakly correlated with CRC, whereas smoking prevalence and alcohol consumption had no effects on the models. The PCC between NAT2 and CRC incidence was 0.46 in males and 0.48 in females when meat consumption was included in the model, compared to 0.14 and 0.15, respectively, when it was not. These data suggest that, in combination with meat intake, some proportion of the international variability in CRC incidence may be attributable to genetic susceptibility to heterocyclic amines, as determined by NAT2 genotype.

The purpose of this study was to determine whether pre-B-cell colony-enhancing factor is a secreted cytokine in the human amnion and to study its chemotaxic and antiapoptotic properties.Pre-B-cell colony-enhancing factor secretion was studied from amniotic epithelial-like WISH cells and primary amniotic epithelial cells that were seeded on squares of immobilon-P membrane and stimulated with lipopolysaccharide or tumor necrosis factor-alpha, respectively. The pre-B-cell colony-enhancing factor protein was detected both intracellularly and after secretion, as bound to the membrane, by immunostaining and densitometry. Medium and cell lysates that were obtained from WISH cells that were treated with lipopolysaccharide alone or together with a pre-B-cell colony-enhancing factor antisense oligonucleotide to block pre-B-cell colony-enhancing factor translation were also analyzed for secreted pre-B-cell colony-enhancing factor by Western blotting and densitometry. A chemotaxic effect of pre-B-cell colony-enhancing factor on human neutrophils was compared with the chemoattractants interleukin-8 and N-Formyl-Met-Leu-Phe methyl ester in a rapid fluorescence-based neutrophil migration assay. Apoptosis was induced in primary amniotic epithelial cells and fibroblasts by actinomycin D (1 microg/mL); the antiapoptotic effects of pre-B-cell colony-enhancing factor on early apoptosis were measured by the annexin V assay, and the late effects were determined by measurement of nuclear matrix protein in the media.Treatment of amnion cells that adhered to immobilon-P membrane to induce the secretion of pre-B-cell colony-enhancing factor showed significantly (P.05) more pre-B-cell colony-enhancing factor protein surrounding the cells compared with the controls. Although the addition of lipopolysaccharide to cultured WISH cells caused the secretion of pre-B-cell colony-enhancing factor into the medium, co-treatment with an antisense oligonucleotide to pre-B-cell colony-enhancing factor obliterated it. Analysis of the cell lysates showed no significant change, which suggests that most of the pre-B-cell colony-enhancing factor protein had been secreted. No significant chemotaxic effects of pre-B-cell colony-enhancing factor were observed; however, pre-B-cell colony-enhancing factor treatment (100 ng/mL), together with actinomycin D, cancelled the early induction of apoptosis, although there was a dose-dependent and significant late antiapoptotic effect on primary amnion epithelial cells (P.001) and fibroblasts (P.01).Pre-B-cell colony-enhancing factor is a secreted protein from amniotic epithelial cells. Although it had no chemotaxic effects, it was antiapoptotic for both amniotic epithelial cells and fibroblasts and may protect these cells against apoptosis that is induced by chronic distension, labor, or infection.

Objective: Our purpose was to determine whether pre-B-cell colony-enhancing factor (PBEF) is expressed in the human fetal membranes during normal gestation and parturition in the absence of infection and to show its effects on the expression of interleukin (IL)-6 and IL-8. Study Design: PBEF was immunolocalized in the fetal membranes from early pregnancy, at preterm, and at term. Its expression was quantitated by Northern analysis in separated uninfected amnion, chorion, decidua, and placenta of patients at term before labor and in full-thickness membranes before and after spontaneous labor at preterm and at term. Amnion-like epithelial (WISH) cells and fetal membrane explants were treated with recombinant PBEF (rhPBEF), and the expression of IL-6 and IL-8 was quantitated. Results: PBEF was immunolocalized throughout gestation in the amniotic epithelium and mesenchymal cells as well as the chorionic cytotrophoblast and parietal decidua. Northern analysis showed significantly more (P

Pre-B-cell colony enhancing factor (PBEF) was first isolated from an activated peripheral blood lymphocyte cDNA library and was found to be involved in the maturation of B-cell precursors. It was subsequently identified as one of the genes upregulated by distending the human fetal membranes in vitro. Here we report on the genomic organization of this gene, which is composed of 11 exons and 10 introns, spanning 34.7 kb of genomic DNA. Neither the gene nor the protein has any homology with other cytokines in any currently available database. The use of two promoters (proximal and distal) may result in differential, tissue specific expression of the PBEF transcripts. The 5'-flanking region lacks the classical sequence motif that would place it with the hematopoietic cytokines; however, it has several putative regulatory elements, suggesting that this gene may be chemically and mechanically responsive to inducers of transcription. The three PBEF mRNA transcripts were observed in both normal and infected human fetal membranes but were significantly upregulated (P

Although little is known about etiology of childhood rhabdomyosarcoma, early life factors are suspected in the etiology. We explored this hypothesis using linked data from the California Cancer Registry and the California birth rolls. Incident cases were 359 children < 6 year old (218 embryonal, 81 alveolar, 60 others) diagnosed in 1988-2008. Controls (205,173), frequency matched on birth year (1986-2007), were randomly selected from the birth rolls. We examined association of birth characteristics such as birth weight, size for gestational age, and timing of prenatal care with all-type rhabdomyosarcoma, embryonal and alveolar subtypes. Crude and adjusted odds ratios (ORs) and 95% confidence intervals (95% CIs) were estimated using logistic regression. In contrast to a previous study, we observed statistically non-significant association for embryonal subtype among high birth weight (4000-5250 grams) children for term births [OR (95%CI): 1.28 (0.85, 1.92)] and all births adjusted for gestational age [OR (95%CI): 1.21 (0.81, 1.81)]. On the other hand, statistically significant 1.7-fold increased risk of alveolar subtype (95%CI: 1.02, 2.87) was observed among children with late or no prenatal care and a 1.3-fold increased risk of all rhabdomyosarcoma subtypes among children of fathers ≥ 35 years old at child birth (95%CI: 1.00, 1.75), independent of all covariates. Our finding positive association on male sex for all rhabdomyosarcoma types is consistent with previous studies. While we did not find a convincingly positive association between high birth weight and RMS, our findings on paternal age at childbirth and prenatal care supports the hypothesis that prenatal environment modifies risk for childhood rhabdomyosarcoma.

Background Earlier, we reported a highly statistically significant association between T-helper 1 (Th1) and Th2 cytokine genotypes and hepatocellular carcinoma (HCC) risk among natives of southern Guangxi, China, a hyperendemic region for HCC. Epidermal growth factor (EGF) plays a critical role in malignant transformation of hepatocytes and tumor progression. A polymorphism in the EGF gene (61A > G) results in elevation of EGF in liver tissues and blood. Epidemiological data are sparse on the possible association between EGF genetic polymorphism and HCC risk. Methods The EGF 61A > G polymorphism, multiple Th1 and Th2 genotypes, and environmental risk factors for HCC were determined on 117 HCC cases and 225 healthy control subjects among non-Asians of Los Angeles County, California, a low-risk population for HCC, and 250 HCC cases and 245 controls of southern Guangxi, China. Results Following adjustment for all known or suspected HCC risk factors, non-Asians in Los Angeles who possessed at least one copy of the high activity 61*G allele of the EGF gene showed a statistically non-significant, 78% increased risk of HCC compared with those possessing the EGF A/A genotype. This EGF-HCC risk association significantly strengthened among heavy users of alcohol [odds ratio (OR) = 3.44, 95% confidence interval (CI) = 0.93–12.76, P = 0.065)], and among individuals carrying the high-risk Th1/Th2 genotypes for HCC (OR = 3.34, 95% CI = 1.24-9.03, P = 0.017). No association between EGF genotype and HCC risk was observed among Chinese in southern Guangxi, China. Conclusion Genetic polymorphism in the EGF gene resulting in elevated level of EGF, may contribute to HCC risk among low-risk non-Asians in Los Angeles.

It is well established that cancers are caused by the accumulation of genomic and epigenomic alterations. However, molecular changes occuring in the early stages of cancer development or in precursor lesions remain to be poorly understood.The employment of molecular characterization of tumors prior to therapy has opened the door for personalized therapy of individual patients. Such genetic alterations that are utilized to predict response to therapy are considered predictive biomarkers. The development of high throughput technologies lead to the establishment of a relatively new field of cancer genomics. These genome-wide approaches are increasingly more important in cancer diagnostic, prognosis, and treatment. Here we briefly discuss cancer transcriptome, cancer genome and epigenome analyses approches and their clinical utility. Gene expression patterns in tumors (cancer transcriptome) are analyzed by expression microarrays who can serve as a diagnostic tool which facilitates distinguishing different cancer subtypes. Another high throughput technology that may revolutionize personalized cancer therapy, lead to the development of new genetic diagnostic tests and biomarkers is next generation sequencing (NGS). NGS has an ability to fully sequence large number of genes in a single test and simultaneously detect deletions, insertions, copy number alterations, translocations and exome-wide base substitutions in cancer-related genes. NGS methods analyses DNA methylation, detection of modified histones, mapping of transcription factor occupancy, and epigenetic regulators. DNA diagnosis often trumps clinical diagnosis in oncology. This will cause the shift toward testing minute amounts of DNA and specimens including needle biopsies, circulating tumor cells, and ciruclating cell-free DNA are likely to become clinically relevant. Thus, as NGS enters clinical testing it will impact clinical decisions and cancer outcomes. Finally, improved understanding of cancer biology will lead to further development of targeted therapies and the use of combinations of targeted approaches simultaneously, increasing treatment effectiveness and supporting highly individualized patient care.

Over 100 single nucleotide polymorphisms (SNP) are validated in the TP53 tumor suppressor gene. They define haplotypes, which may differ in their activities. Therefore, mutation in cancer may occur at different rates depending upon haplotypes. However, these associations may be masked by differences in mutations types and causes of mutagenesis. We have analyzed the associations between 19 SNPs spanning the TP53 locus and a single specific aflatoxin-induced TP53 mutation (R249S) in 85 in hepatocellular carcinoma cases and 132 controls from Thailand. An association with R249S mutation (P = 0.007) was observed for a combination of two SNPs (rs17882227 and rs8064946) in a linkage disequilibrium block extending from upstream of exon 1 to the first half of intron 1. This domain contains two coding sequences overlapping with TP53 (WRAP53 and Hp53int1) suggesting that sequences in TP53 intron 1 encode transcripts that may modulate R249S mutation rate in HCC.

Although rare, synovial sarcoma (SS) is one of the most common soft tissue sarcomas affecting young adults. To investigate potential tumor markers related to synovial sarcoma prognosis, we carried out a single-institution retrospective analysis of 103 patients diagnosed with SS between 1980 and 2009. Clinical outcome data were obtained from medical records, and archived tissue samples were used to evaluate the relationship between progression-free survival (PFS) and several prognostic factors, including tumor expression of FGFR3 and FGFR4. No associations were found between PFS and gender, body mass index, tumor site, SS18-SSX translocation, or FGFR4 expression. As seen in previous studies, age at diagnosis (5 cm, 22% 10-year PFS; P < .0001) were associated with PFS in SS patients. In addition, in a subset of patients with available archived tumor samples taken prior to chemotherapy or radiation (n = 34), higher FGFR3 expression was associated with improved PFS (P = .030). To the best of our knowledge, this is the largest study of SS to date to suggest a potential clinical role for FGFR3. While small numbers make this investigation somewhat exploratory, the findings merit future investigation on a larger scale.

The tumor suppressor gene TP53 is the most commonly mutated gene in human cancer. The reported prevalence of mutations in rhabdomyosarcoma (RMS) varies widely, with recent larger studies suggesting that TP53 mutations in pediatric RMS may be extremely rare. Overexpression of MDM2 also attenuates p53 function. We have performed TP53 mutation/ MDM2 amplification analyses in the largest series analyzed thus far, including DNA isolated from 37 alveolar and 38 embryonal RMS tumor samples obtained from the Cooperative Human Tissue Network (CHTN). Available samples were frozen tumor tissues ( ) and histopathology slides. TP53 mutations in exons 4–9 were analyzed by direct sequencing in all samples, and MDM2 amplification analysis was performed by differential PCR on a subset of 22 samples. We found only one sample (1/75, 1.3%) carrying a TP53 mutation at codon 259 (p.D259Y) and no MDM2 amplification. Two SNPs in the TP53 pathway, associated with accelerated tumor onset in germline TP53 mutation carriers, ( TP53 SNP72 (rs no. 1042522) and MDM2 SNP309 (rs no. 2279744)), were not found to confer earlier tumor onset. In conclusion, we confirm the extremely low prevalence of TP53 mutations/ MDM2 amplifications in pediatric RMS (1.33% and 0%, respectively). The possible inactivation of p53 function by other mechanisms thus remains to be elucidated.

Non–small-cell lung carcinoma (NSCLC) (n = 65) were analyzed for promoter methylation of RASSF1A, CDH13, MGMT, ESR1, and DAPK genes in matching lung tumors, normal lung tissue, and blood samples. Aberrant methylation in CDH13 and MGMT was associated with clinicopathologic features of NSCLC. Hypermethylation detected in primary tumors was not observed in corresponding blood samples, which rendered this an unsuitable blood-based test for NSCLC detection.Systemic methylation changes may be a diagnostic marker for tumor development or prognosis. Here, we investigate the relationship between gene methylation in lung tumors relative to normal lung tissue and whether DNA methylation changes can be detected in paired blood samples.Sixty-five patients were enrolled in a surgical case series of non-small-cell lung carcinoma at a single institution. By using bisulfite pyrosequencing, CpG methylation was quantified at 5 genes (RASSF1A, CDH13, MGMT, ESR1, and DAPK) in lung tumor, pathologically normal lung tissue, and circulating blood from enrolled cases.The analyses of methylation in tumors compared with normal lung tissue identified higher methylation of CDH13, RASSF1A, and DAPK genes, whereas ESR1 and MGMT methylation did not differ significantly between these tissue types. We then examined whether the 3 aberrantly methylated genes could be detected in blood. The difference in methylation observed in tumors was not reflected in methylation status of matching blood samples, which indicated a low feasibility of detecting lung cancer by analyzing these genes in a blood-based test. Lastly, we probed whether tumor methylation was associated with clinical and demographic characteristics. Histology and sex were associated with methylation at the CDH13 gene, whereas, stage was associated with methylation at MGMT.Our results showed higher methylation of RASSF1A, CDH13, and DAPK genes in lung tumors compared with normal lung. The lack of reflection of these methylation changes in blood samples from patients with non-small-cell lung carcinoma indicates their poor suitability for a screening test.

Although inflammation is primarily a homeostatic response of tissues to damage by infectious, physical, or chemical agents, its persistence in a chronic form generates a profoundly modified environment that favors the occurrence of transformed cells and their progression to malignant cancer. Chronic inflammation is one of the hallmarks of most solid tumors and is a precursor condition in a wide range of pathologies including cancers of the colon, esophagus, stomach, or bladder. Chronic inflammation is characterized by persistent attraction of immune cells secreting specific mediators at the site of the lesions. These mediators include DNA-damaging radicals and cytokines and chemokines that enhance proliferation, stimulate the development of stromal cells, downregulate apoptosis, increase neo-angiogenesis and facilitate cell motility and invasion. Cytokines are produced in a large variety of forms with overlapping biological effects, operating within complex signaling networks. Of particular importance in cancer are interleukin-1 (IL-1), IL-6, tumor necrosis factor α (TNFα), chemokines and their receptors, as well as receptors of the death domain family. Resident cells at inflammatory sites adapt by producing factors that enhance their survival. One of these factors is cyclooxygenase-2 (COX-2), which is controlled by the interplay between p53 and nuclear factor kappa B (NFκB), two factors with broad roles in inflammatory responses. Thus, cancer may be seen as the consequence of a failure of a response primarily geared at wound healing. The mediators of inflammation offer a wide range of potential targets for preventive or therapeutic interventions.

Chronic inflammation, which is suspected to play a role in the development of colorectal cancer (CRC), has rarely been studied in colorectal adenoma. We investigated the inter-relationships of serum levels of the inflammatory proteins CRP and in IL-6, single nucleotide polymorphisms (SNPs) in the CRP (rs1205, rs1130864, rs1800947) and IL6 (rs1800795) genes, and lifestyle factors with colorectal adenoma in a sigmoidoscopy-based case–control study of 271 adenoma cases and 539 age-, sex-, and race/ethnicity-matched controls in Hawaii. We found no association of serum CRP or IL-6 levels with the risk of adenoma. A multiple regression with stepwise selection identified elevated BMI, Caucasian and Native Hawaiian versus Japanese race/ethnicity, and current smoking as being associated with significantly higher serum CRP and IL-6 levels. Female versus male gender was also associated with higher CRP levels and older age with higher IL-6 levels. The C allele of rs1205 and the A allele of rs1130864 were significantly associated with higher serum CRP levels (p trend: 0.0002 and 0.01, respectively), as well as with a decreased adenoma risk [rs1205: OR for CT and CC vs. TT = 0.69 (95% CI: 0.48–0.98) and 0.53 (0.34–0.83), respectively, p trend = 0.008; rs1130864: OR for GA and AA versus GG = 0.65 (0.45–0.93) and 0.74 (0.31–1.76), respectively, p trend = 0.04]. The findings of lower serum CRP and IL-6 levels in Japanese (a group with a high CRC risk) and of a decreased adenoma risk observed for alleles associated with higher circulating CRP levels suggest a protective effect for CRP in early colorectal neoplasia that warrants further study.

Polymorphisms in cytokine genes responsible for inflammatory and immune responses are associated with risk of hepatocellular carcinoma (HCC) in high-risk Chinese population. Similar data in low-risk populations are lacking. A population-based case-control study of HCC was conducted including 120 HCC patients and 230 matched control subjects of non-Asian residents in Los Angeles County, California. Genetic variants in the interferon gamma (IFNgamma), tumor necrosis factor-alpha (TNFalpha), interleukin-2 (IL-2), IL-4, IL-6, IL-10, IL-12 and IL-18 genes were determined by Taqman assays. The logistic regression method was used to analyze the data. For T helper (Th) 1 genes (IFNgamma, IL-6 and IL-12), relative to the putative high-activity genotypes, individual low-activity genotypes were associated with statistically non-significant increases in HCC risk. The odds ratio (OR) was 1.53 [95% confidence interval (CI) = 0.53-4.39] for three versus zero low-activity genotypes. For Th2 cytokines (IL-4 and IL-10), low- versus high-activity genotypes were associated with statistically non-significant decreases in HCC risk. The OR was 0.64 (95% CI = 0.27-1.55) for two versus zero low-activity genotypes. When the Th1 and Th2 genotypes were examined simultaneously, the highest level of risk was observed in individuals jointly possessing the highest number of low-activity Th1 genotypes and the lowest number of low-activity Th2 genotypes. There was a roughly doubling of risk between these two extreme genetic profiles, which did not reach statistical significance (OR = 1.98, 95% CI = 0.50-7.84, P = 0.08). In contrast to high-risk Chinese, Th1 and Th2 genotypes did not impact in a major way on risk of HCC in USA non-Asians.

This is initial study of a gene signatures responsible for adapting microscopic life to the life in extreme Earth environments. We present a results on ID of the clusters of COGs common to several hyperthermophiles and exclusion of those common to a mesophile: E.coli.K12, will yield a group of proteins possibly involved in adaptation to life under extreme T. Methanogens stand out as the only group of organisms that have species capable of growth at 0C (M.frigidum and M.burtonii) and 110C (M.kandleri). Not all the components of heat adaptation can be attributed to novel genes, the chaperones known as heat shock proteins stabilize the enzymes under elevated temperature. Highly conserved chaperons found in bacteria and eukaryots are not present in hyperthermophilic Archea, rather, they have a unique chaperone TF55. Our aim is to use software which we specifically developed for extremophile genome comparative analyses in order to search for additional novel genes involved in hyperthermophile adaptation. The following hyperthermophile genomes incorporated in our software were used for these studies: M.jannaschii, M.kandleri, A.fulgidus and 3 species of Pyrococcus. Common genes were annotated and grouped according to their roles in cellular processes when information was available and proteins not previously implicated in the heat-adaptation of hyperthermophiles were identified. Additional experimental data is needed in order to learn more about these proteins. To address a non-gene based components of thermal adaptation, all sequenced extremophiles were analysed for their GC contents and aminoacid hydrophobicity. We develop a prediction model for optimal growth temperature., Comment: 6 pages, 1 figure, To be published in Serbian Astronomical Journal

Maternal smoking while pregnant is a plausible risk factor for childhood cancers because many seem to initiate in utero and tobacco-specific carcinogens cross the placenta. Social desirability bias may affect maternal report of smoking in case-control studies and could explain inconsistently observed associations with offspring cancer. Detection of tobacco smoke biomarkers in dried blood spots (DBS), which are increasingly stored by newborn screening programs, may improve retrospective assessment of fetal tobacco exposure. As proof-of-principle, we examined cotinine in DBS of 20 infants enrolled in a pilot study of pregnancy among low-income women. We recruited 107 pregnant women (

Objective To determine whether interleukin-6 (IL-6) trans-signaling directs the expression of pre-B cell colony-enhancing factor (PBEF) in vitro and in vivo. Methods Complementary DNA from rheumatoid arthritis (RA) synovial fibroblasts treated with IL-6 and soluble IL-6 receptor (sIL-6R) was used to probe a cytokine microarray. PBEF regulation by the IL-6-related cytokines, IL-6, sIL-6R, oncostatin M (OSM), IL-11, and leukemia inhibitory factor (LIF) was determined by reverse transcription-polymerase chain reaction analysis. IL-6-mediated STAT-3 regulation of PBEF was determined using a cell-permeable STAT-3 inhibitor peptide. Antigen-induced arthritis (AIA) was induced in wild-type (IL-6+/+) and IL-6-deficient (IL-6-/-) mice. PBEF and STAT were detected by immunohistochemistry, immunoblotting, and electrophoretic mobility shift assay. Synovial levels of PBEF were quantified by enzyme immunoassay. Results IL-6 trans-signaling regulated PBEF in a STAT-3-dependent manner. In addition, PBEF was regulated by the IL-6-related cytokine OSM, but not IL-11 or LIF. Flow cytometric analysis of the IL-6-related cognate receptors suggested that OSM regulates PBEF via its OSM receptor and not its LIF receptor. The involvement of PBEF in arthritis progression was confirmed in vivo, where induction of AIA resulted in a 4-fold increase in the synovial expression of PBEF. In contrast, little or no change was observed in IL-6-/- mice, in which the inflammatory infiltrate was markedly reduced and synovial STAT-1/3 activity was also impaired. Analysis of human RA synovial tissue confirmed that PBEF immunolocalized in apical synovial membrane cells, endothelial cells, adipocytes, and lymphoid aggregates. Synovial fluid levels of PBEF were significantly higher in RA patients than in osteoarthritis patients. Conclusion Experiments presented herein demonstrate that PBEF is regulated via IL-6 trans-signaling and the IL-6-related cytokine OSM. PBEF is also actively expressed during arthritis. Although these data confirm an involvement of PBEF in disease progression, the consequence of its action remains to be determined.

Our purpose was to show the effects of pre-B-cell colony-enhancing factor on the genes that are expressed by the human fetal membranes.Explants of fetal membranes (amnion, chorion, and decidua) from three term patients were treated with 100 ng/mL recombinant human pre-B-cell colony-enhancing factor for 4 hours. RNAs were hybridized to gene chips that contained18,000 known genes. One experiment was done in triplicate to assess replication. Data were analyzed to quantitate the signal intensities of each complementary DNA on the array. Confirmation of the results was carried out on tissues from nine other patients by the measurement of the proteins or quantitative real-time reverse transcriptase-polymerase chain reaction.Replication gave92.6% identical results, which showed high method reproducibility. Pre-B-cell colony-enhancing factor treatment caused a significant increase in 103 genes and decrease in 139 genes. Only 8 genes were up-regulated consistently and significantly in all three patients (three key inflammatory cytokines [tumor necrosis factor-alpha, interleukin-6, and interleukin-1beta], four important chemokines [macrophage inflammatory protein-1alpha, macrophage inflammatory protein-1beta, macrophage inflammatory protein-3alpha, and growth-related oncogene-gamma], and prostaglandin-endoperoxide synthase 2). These data were confirmed by the measurement in the media with the use of specific enzyme-linked immunosorbent assays for tumor necrosis factor-alpha, interleukin-6, and interleukin-1beta, macrophage inflammatory protein-1alpha, macrophage inflammatory protein-1beta, and macrophage inflammatory protein-3alpha and by quantitative real-time reverse transcriptase-polymerase chain reaction for growth-related oncogene-gamma and prostaglandin-endoperoxide synthase 2.Pre-B-cell colony-enhancing factor appears to be at the proximal end of the pathway to labor initiation and may link sterile distention-induced labor with that of infection-induced labor.

1576 Background: Fibrosarcoma (FS) is the second most common group of soft tissue sarcomas in children, however, most FS are diagnosed in adults. The goal of this study was to compare clinical features and outcomes of children and adults diagnosed with FS and identify predictors of survival. Methods: We have analyzed data from 569 children (≤ 19 years) and 5,508 adults (>19 years) diagnosed between 1973 and 2008 with FS (ICCC category IXb) available in the SEER database. Survival estimates were determined using survival time with end point death from any cause. Results: Comparison of two diagnostic periods, 1973-1989 vs. 1990-2008 showed that 5-year survival rates have improved in adults (48.4% vs 60.9%, P

Background: Rhabdomyosarcoma (RMS) is the most common type of soft-tissue sarcoma among 0-19 year olds, with the incidence rate highest among children of ages 0-4. Since, childhood cancers tend to have relatively shorter lag time between exposure and disease, early childhood cancer such as RMS could be due to exposures during pregnancy or early infancy. Very little is known about environmental factors that may increase the susceptibility to RMS. Two major subtypes_embryonal and alveolar_have been linked with overexpression of the gene encoding insulin-like growth factor 2 (IFG2), which is also associated with fetal overgrowth syndrome. A couple of studies have suggested accelerated fetal growth as a risk factor, but needs to be confirmed. We examined associations between fetal growth measures and all RMS, and separately for the two major subtypes. We also examined other prenatal/perinatal factors including prenatal care, parental age, and parity. Methods: We conducted a population based case-control study in California by linking California Cancer registry and birth certificate data. Incident cases in children 0-5 ages (overall n=359, embryonal RMS=218, alveolar RMS=81) diagnosed in 1988-2008 and controls, frequency matched on birth year (1986-2007, n=205,230) were included. Logistic regression was applied to examine the associations of interest in crude and adjusted models. Results: The point estimates in adjusted models suggested an increased risk for embryonal RMS for all fetal growth measures employed, i.e., high birthweight (4000-5250 gms) at term births only, for high birth weight (4000-5250 gms) adjusted for gestational age, and large for gestational age births (OR (95%CI): 1.28 (0.85, 1.92); 1.21 (0.81, 1.81); 1.13 (0.73, 1.75) respectively), but not for alveolar RMS or overall RMS cases. We found increased risk for alveolar RMS among those with prenatal care starting after the first trimester or no care at all compared to prenatal care in the first trimester (OR(95%CI): 1.68 (1.01, 2.80)). Findings for other factors including higher risk among male and higher parental age at child birth were consistent with findings from existing studies. Conclusion: We did not find a convincingly positive association between fetal growth and RMS, although our data suggested small risk increases particularly for embryonal RMS. However, our findings on starting time of prenatal care and parental age at childbirth further support the notion that the early fetal/embryonic environment may be important for developing RMS in early childhood. Larger studies examining well-measured early life environment that may cause genetic and epigenetic alteration observed in RMS cases are needed to improve our understanding of the RMS etiology. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 665. doi:1538-7445.AM2012-665

Sarcoma plays a central role in Li-Fraumeni syndrome (LFS) definition. Germline mutations in TP53 gene underlie this rare familial syndrome and are detected in over 80% of LFS patients. The International Agency for Research on Cancer (IARC) maintains a database of germline TP53 mutations that collects published data on LFS and related syndromes and provides baseline information about TP53 mutation prevalence and phenotype in these patients. We analyzed the characteristics of germline TP53 germline mutations in LFS and related syndrome patients with sarcoma using the IARC TP53 Database. The prevalence of individual sarcoma types and their age/gender distribution in TP53 mutation carriers were compared to sporadic sarcomas in Caucasians obtained by SEER registry analysis using the SEERStat program. Sarcoma represented 25% of all tumors diagnosed in TP53 carriers in this study. We confirmed young age of sarcoma onset among carriers, with 95.6% of cases diagnosed before the age of fifty years, as opposed to 38.3% of sporadic cancer. Carriers had increased risk for osteosarcoma in both children/adolescents and adults (OR=1.41, 95% CI=1.02-1.94, and OR=4.61, 95% CI=2.72-7.83), while increased risk for rhabdomyosarcoma was confined to carriers younger than 5 years (OR=11.6, 95%CI=6.1-21.9, p In conclusion, this study provided further evidence for genotype-phenotype correlations in germline TP53 mutations carriers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5538. doi:10.1158/1538-7445.AM2011-5538

Background The International Study on Embryonal Tumours (ISET) was initiated by epidemiologists and pediatric clinicians in 13 countries worldwide including 7 in Europe (UK, the Netherlands, Italy France, Serbia, Macedonia, Czech Republic), 3 in America (California USA, Canada, Brazil), and 3 in Asia / Oceania (India, Japan, and Australia), in collaboration with the International Agency for Research on Cancer. The study is focused on the etiology of non-CNS embryonal tumors which have been severely under-studied to date. Due to their rarity, past studies of these tumors have been underpowered and an international effort is required to accrue sufficient numbers of cases. The full study will include retinoblastoma, Wilms tumor, rhabdomyosarcoma, neuroblastoma and hepatoblastoma. Our main objective is to conduct a comprehensive study to investigate the effect of perinatal factors, molecular profiles and gene-environment interaction on the risk of these tumors. Methods This study is based on a case-control trio design, which has been shown to be a powerful design for genetic association and it is robust against the bias due to population stratification. For childhood cancer, the parent-child trio design is particularly appropriate as it can be used to study maternal-fetal effects and parent of origin such as imprinting. We collect information on parental environmental exposure history, medical and family history, as well as data on neonatal and infancy history of the index child by detailed interview with a standardized questionnaire. We obtain DNA samples from the trios. Tumor samples will also be collected in collaboration with clinical trials groups for disease characterization. We plan to investigate the effect of perinatal factors and incorporate molecular profiles of the trios such as epigenetic aberration, germline variation and DNA repair capacity, to conduct comprehensive investigations on gene-environment interactions. Results The pilot study of Wilms tumor and neuroblastoma has been launched in Australia, France, Czech Republic, Serbia, Macedonia and Canada in 2009 and 2010. The estimated number of patients to be recruited varies by study center and cancer site, with a total of approximately 1400 per year (including 640 Wilms tumor and 400 neuroblastoma). The participation rate for case trios is between 70-80%, and among the participating families, more than 95% are willing to provide biological samples. The results of the pilot study will be presented. The pilot results also indicate that the adjustment of study protocol and questionnaire to local requirement is necessary for multicenter study at international scale. Discussion ISET Investigators aim to improve the understanding of etiology and pathogenesis of these tumors, providing new tools for their prevention and control. Greater understanding of factors leading to the development of these tumors may improve surveillance, diagnosis, prognosis, and treatment of these childhood malignancies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1821.