Extensive sequence variation in the 3′ untranslated region of the KRAS gene in lung and ovarian cancer cases

While cancer is a serious health issue, there are very few genetic biomarkers that predict predisposition, prognosis, diagnosis, and treatment response. Recently, sequence variations that disrupt microRNA (miRNA)-mediated regulation of genes have been shown to be associated with many human diseases, including cancer. In an early example, a variant at one particular single nucleotide polymorphism (SNP) in a let-7 miRNA complementary site in the 3′ untranslated region (3′ UTR) of the KRAS gene was associated with risk and outcome of various cancers. The KRAS oncogene is an important regulator of cellular proliferation, and is frequently mutated in cancers. To discover additional sequence variants in the 3′ UTR of KRAS with the potential as genetic biomarkers, we resequenced the complete region of the 3′ UTR of KRAS in multiple non-small cell lung cancer and epithelial ovarian cancer cases either by Sanger sequencing or capture enrichment followed by high-throughput sequencing. Here we report a comprehensive list of sequence variations identified in cases, with some potentially dysregulating expression of KRAS by altering putative miRNA complementary sites. Notably, rs712, rs9266, and one novel variant may have a functional role in regulation of KRAS by disrupting complementary sites of various miRNAs, including let-7 and miR-181.     

Combined effect of GSTM1, GSTT1 and GSTP1 polymorphisms on histological subtypes of lung cancer

Genetic polymorphisms are natural genetic variations in the gene sequence that occur at a frequency of >1% in the population. This genetic variability (polymorphisms) can be a factor in cancer risk. The functional polymorphisms in GST genes play an important role in susceptibility to lung cancer. In our previous study, we reported that the combination of certain genotypes of GSTM1, GSTT1 and CYP1A1 is associated with lung cancer. The study has been extended to investigate the potential role of polymorphism in GSTP1 alone or in combination with the status of GSTM1 and GSTT1 genes in the likelihood of development of lung cancer. A total of 302 subjects (151 cases and 151 controls) were evaluated. Using a case–control design, individuals were genotyped for GSTs using multiplex polymerase chain reaction and restriction fragment length polymorphism techniques. The data obtained were analyzed using multiple logistic regression. The combined ‘at risk’ genotypes of GSTM1 null and GSTT1 null in comparison with ‘wild-type’ genotypes seems to be associated with a greater risk of lung cancer, but the results are not significant (odds ratio (OR) 2.0, 95% confidence interval (CI) 0.68–5.96) and for squamous cell carcinoma (SqCC) it was 1.6-fold (OR 1.6, 95% CI 0.49–5.68). In summary, our case–control study of lung cancer revealed that the effect of these polymorphisms is not very marked for different genotypic combinations of GSTP1, GSTM1 and GSTT1 in the context of developing lung cancer in a north Indian population. However, the increased risk was limited to SqCC, and was not found for other histological subtypes. Further analyses on this topic are needed.     

Serum proteome mapping of EGF transgenic mice reveal mechanistic biomarkers of lung cancer precursor lesions with clinical significance for human adenocarcinomas

Atypical adenomatous hyperplasia (AAH) of the lung is a pre-invasive lesion (PL) with high risk of progression to lung cancer (LC). However, the pathways involved are uncertain. We searched for novel mechanistic biomarkers of AAH in an EGF transgenic disease model of lung cancer. Disease regulated proteins were validated by Western immunoblotting and immunohistochemistry (IHC) of control and morphologically altered respiratory epithelium. Translational work involved clinical resection material. Collectively, 68 unique serum proteins were identified by 2DE-MALDI-TOF mass spectrometry and 13 reached statistical significance (p?<?0.05). EGF, amphiregulin and the EGFR endosomal sorting protein VPS28 were induced up to 5-fold while IHC confirmed strong induction of these proteins. Furthermore, ApoA1, α-2-macroglobulin, and vitamin-D binding protein were nearly 6- and 2-fold upregulated in AAH; however, ApoA1 was oppositely regulated in LC to evidence disease stage dependent regulation of this tumour suppressor. Conversely, plasminogen and transthyretin were highly significantly repressed by 3- and 20-fold. IHC confirmed induced ApoA1, Fetuin-B and transthyretin expression to influence calcification, inflammation and tumour-infiltrating macrophages. Moreover, serum ApoA4, ApoH and ApoM were 2-, 2- and 6-fold repressed; however tissue ApoM and sphingosine-1-phosphate receptor expression was markedly induced to suggest a critical role of sphingosine-1-phosphate signalling in PL and malignant transformation. Finally, a comparison of three different LC models revealed common and unique serum biomarkers mechanistically linked to EGFR, cMyc and cRaf signalling. Their validation by IHC on clinical resection material established relevance for distinct human lung pathologies. In conclusion, we identified mechanistic biomarker candidates recommended for in-depth clinical evaluation.     

DNA methylation changes in atypical adenomatous hyperplasia, adenocarcinoma in situ, and lung adenocarcinoma

Background

Aberrant DNA methylation is common in lung adenocarcinoma, but its timing in the phases of tumor development is largely unknown. Delineating when abnormal DNA methylation arises may provide insight into the natural history of lung adenocarcinoma and the role that DNA methylation alterations play in tumor formation.

Methodology/Principal Findings

We used MethyLight, a sensitive real-time PCR-based quantitative method, to analyze DNA methylation levels at 15 CpG islands that are frequently methylated in lung adenocarcinoma and that we had flagged as potential markers for non-invasive detection. We also used two repeat probes as indicators of global DNA hypomethylation. We examined DNA methylation in 249 tissue samples from 93 subjects, spanning the putative spectrum of peripheral lung adenocarcinoma development: histologically normal adjacent non-tumor lung, atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS, formerly known as bronchioloalveolar carcinoma), and invasive lung adenocarcinoma. Comparison of DNA methylation levels between the lesion types suggests that DNA hypermethylation of distinct loci occurs at different time points during the development of lung adenocarcinoma. DNA methylation at CDKN2A ex2 and PTPRN2 is already significantly elevated in AAH, while CpG islands at 2C35, EYA4, HOXA1, HOXA11, NEUROD1, NEUROD2 and TMEFF2 are significantly hypermethylated in AIS. In contrast, hypermethylation at CDH13, CDX2, OPCML, RASSF1, SFRP1 and TWIST1 and global DNA hypomethylation appear to be present predominantly in invasive cancer.

Conclusions/Significance

The gradual increase in DNA methylation seen for numerous loci in progressively more transformed lesions supports the model in which AAH and AIS are sequential stages in the development of lung adenocarcinoma. The demarcation of DNA methylation changes characteristic for AAH, AIS and adenocarcinoma begins to lay out a possible roadmap for aberrant DNA methylation events in tumor development. In addition, it identifies which DNA methylation changes might be used as molecular markers for the detection of preinvasive lesions.     

肺癌患者与肺结核患者血清蛋白的电泳分析

采用SDS聚丙烯酰胺凝胶电泳银染色的方法,对58例肺癌患者和32例肺结核患者的血清蛋白进行比较分析,发现有五种特异蛋白,分别存在于A区、C区、F区和G区。肺癌组和肺结核组比较,存在极显著性差异(P<0.01),提示有早期诊断肺癌的价值,有可能成为临床诊断肺癌的一个重要参考指标。     

Reduced geographic variation in roars in different habitats rejects the acoustic adaptation hypothesis in the black-and-gold howler monkey (Alouatta caraya)

Vocalizations used for long-range communication must disperse without significant structural changes to be decoded by receivers. The acoustic adaptation hypothesis (AAH) holds that, since acoustic signals are influenced by the habitat in which they disperse, sounds will possess specific structural characteristics to diminish sound degradation. Additionally, vocalizations can also be influenced by genetics, anatomy, and/or cultural aspects. Here, we tested the AAH through quantitative comparisons of roars in four allopatric populations of the black-and-gold howler monkey (Alouatta caraya) across an environmental gradient from open to closed, in northeastern Argentina. At each site, we obtained good-quality recordings from three adult males, also between July and November 2013, conducted vegetation surveys (measuring tree density, canopy closure, and vertical structure), evaluated potential masking of roars by gathering environmental sound samples, and assessed sound attenuation of a synthetic tone at three different distances: 10 m (landmark reference distance), 50, and 100 m. We also tested the alternative hypothesis that acoustic properties of roars could be explained by population genetic divergence. Our results did not support the AAH. Although our four study sites were significantly different in vegetation structure, conforming to an open-to-closed gradient, roars of A. caraya were not different among populations. Likewise, although environmental sound differed between sites, we found no evidence of environmental sound affecting the acoustic properties of roars. The attenuation of the synthetic tone was only near significant at 100 m distance between both extreme sites from the environmental gradient. The four A. caraya study populations grouped into three genetically differentiated clusters. Since roar features were independent from population genetic clustering, we reject the genetic hypothesis too. The combination of high amplitude and low peak frequency of roars, coupled to small home range size and extensive overlap between neighboring groups, allows roars to keep their communication value across habitats without need of specific environmental tuning.     

Testing drivers of acoustic divergence in cicadas (Cicadidae: Tettigettalna)

Divergence in acoustic signals may have a crucial role in the speciation process of animals that rely on sound for intra-specific recognition and mate attraction. The acoustic adaptation hypothesis (AAH) postulates that signals should diverge according to the physical properties of the signalling environment. To be efficient, signals should maximize transmission and decrease degradation. To test which drivers of divergence exert the most influence in a speciose group of insects, we used a phylogenetic approach to the evolution of acoustic signals in the cicada genus Tettigettalna, investigating the relationship between acoustic traits (and their mode of evolution) and body size, climate and micro-/macro-habitat usage. Different traits showed different evolutionary paths. While acoustic divergence was generally independent of phylogenetic history, some temporal variables’ divergence was associated with genetic drift. We found support for ecological adaptation at the temporal but not the spectral level. Temporal patterns are correlated with micro- and macro-habitat usage and temperature stochasticity in ways that run against the AAH predictions, degrading signals more easily. These traits are likely to have evolved as an anti-predator strategy in conspicuous environments and low-density populations. Our results support a role of ecological selection, not excluding a likely role of sexual selection in the evolution of Tettigettalna calling songs, which should be further investigated in an integrative approach.     

Identification of pathological subtypes of early lung adenocarcinoma based on artificial intelligence parameters and CT signs

Objective: To explore the value of quantitative parameters of artificial intelligence (AI) and computed tomography (CT) signs in identifying pathological subtypes of lung adenocarcinoma appearing as ground-glass nodules (GGNs). Methods: CT images of 224 GGNs from 210 individuals were collected retrospectively and classified into atypical adenomatous hyperplasia (AAH)/adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and invasive adenocarcinoma (IAC) groups. AI was used to identify GGNs and to obtain quantitative parameters, and CT signs were recognized manually. The mixed predictive model based on logistic multivariate regression was built and evaluated. Results: Of the 224 GGNs, 55, 93, and 76 were AAH/AIS, MIA, and IAC, respectively. In terms of AI parameters, from AAH/AIS to MIA, and IAC, there was a gradual increase in two-dimensional mean diameter, three-dimensional mean diameter, mean CT value, maximum CT value, and volume of GGNs (all P<0.0001). Except for the CT signs of the location, and the tumor–lung interface, there were significant differences among the three groups in the density, shape, vacuolar signs, air bronchogram, lobulation, spiculation, pleural indentation, and vascular convergence signs (all P<0.05). The areas under the curve (AUC) of predictive model 1 for identifying the AAH/AIS and MIA and model 2 for identifying MIA and IAC were 0.779 and 0.918, respectively, which were greater than the quantitative parameters independently (all P<0.05). Conclusion: AI parameters are valuable for identifying subtypes of early lung adenocarcinoma and have improved diagnostic efficacy when combined with CT signs.     

Association between <Emphasis Type="Italic">GSTM1</Emphasis>, <Emphasis Type="Italic">GSTT1</Emphasis>, and <Emphasis Type="Italic">GSTP1</Emphasis> polymorphisms and lung cancer risk in a Turkish population

Several studies focused on investigating genetic polymorphisms in order to estimate genetic contribution to lung cancer often showed conflicting results. In this study, we investigated the role of GSTM1, GSTT1, GSTP1 exon 5 and exon 6 polymorphisms on developing lung cancer and histological subtypes in 213 lung cancer patients and 231 controls. GSTM1 null, GSTT1 null, and GSTP1 exon 5 variant genotypes did not show a significant risk for developing lung cancer overall. Significant association was noted between GSTP1 exon 6 variant genotypes and overall lung cancer risk (OR 2.17, 95% CI 1.25–3.78; P = 0.006). These results show that GSTP1 exon 6 polymorphism might be an important factor in determining lung cancer susceptibility in a Turkish population.     

Sputum analysis: Non‐invasive early lung cancer detection

Lung cancer is the leading cause of cancer‐related deaths over the world, characterized by a very high mortality rate. Molecular technique development tries to focus on early detection of cancers by studying molecular alterations that characterize cancer cells. Worldwide lung cancer research has focused on an ever‐increasing number of molecular elements of carcinogenesis at genetic, epigenetic and protein levels. The non‐invasiveness is the characteristic that all clinical trials on cancer detection should have. Abnormal chest imaging and/or non‐specific symptoms are initial signals of lung cancer that appear in an advanced stage of disease. This fact represents the cause of the low 5‐year survival rate: over 90% of patients dying within 5 years of diagnosis. Since smokers have higher quantity of sputum containing exfoliated cells from the bronchial tree, and the sputum represents the most easily accessible biological fluid and its collection is non‐invasive, analysis of this sample represents a good area of research in early lung cancer diagnosis. Continued cigarette smoking is the cause of chronic obstructive pulmonary disease (COPD), with an estimated attributable risk factor exceeding 80% in smoking affected individuals. Lung cancer is found in 40–70% of patients with COPD, particularly in severe disease, and it is a common cause of death in these patients. A large prospective trial of almost half a million non‐smokers showed as lung cancer is also common in patients with COPD who have never smoked. This review describes issues related to early lung cancer screening using non‐invasive methods. J. Cell. Physiol. © 2012 Wiley Periodicals, Inc.     

表观遗传学与肺癌

表观遗传是在指不影响遗传序列的情况下影响型状表达的方法。除了经典遗传方面,如点突变、颠换、插入与肺癌的发生有关,近年来研究显示表观遗传学对肺癌的发生也起到了重要的作用。本文主要从表观遗传学角度,简述了DNA甲基化、组蛋白修饰、非编码RNA尤其是mi RNA与肺癌的关系,甲基化主要是通过抑制原癌基因,促进抑癌基因表达导致肺癌,组蛋白修饰会促进抑癌基因的表达,非编码RNA可以作为肺癌诊断的生物标记物,为肺癌的早期诊断提供依据。     

Characterization of the cell of origin for small cell lung cancer

Small cell lung carcinoma (SCLC) is a neuroendocrine subtype of lung cancer that affects more than 200,000 people worldwide every year with a very high mortality rate. Here, we used a mouse genetics approach to characterize the cell of origin for SCLC; in this mouse model, tumors are initiated by the deletion of the Rb and p53 tumor suppressor genes in the lung epithelium of adult mice. We found that mouse SCLCs often arise in the lung epithelium, where neuroendocrine cells are located, and that the majority of early lesions were composed of proliferating neuroendocrine cells. In addition, mice in which Rb and p53 are deleted in a variety of non-neuroendocrine lung epithelial cells did not develop SCLC. These data indicate that SCLC likely arises from neuroendocrine cells in the lung.     

<Emphasis Type="Italic">RASSF1A</Emphasis> expression level in primary epithelial tumors of various locations

Tumor suppressor activity of RASSF1A in vitro and in vivo was established, in particular, in studies of knockout mice cells. Data on methylation of the promoter region and a lower expression of RASSF1A were mostly obtained with cancer cell lines. Here, the RASSF1A mRNA was quantified the first time in primary epithelial malignant tumors of five various locations from 130 patients by semi-quantitative RT-PCR. Representative samples of kidney, lung, and breast carcinomas were examined. Preliminary data were obtained for RASSF1A expression in ovarian and colorectal carcinomas. System studies showed unexpected expression profiles, namely, the mRNA level increased (two- to sevenfold) more frequently than decreased in renal, breast, ovarian, and colorectal carcinomas. A higher RASSF1A mRNA level was significantly more frequent in renal cell carcinomas (24/38, 63% vs 8/38, 21%, P = 0.0004 by Fisher’s exact test) and ovarian carcinomas (8/13, 62% vs 2/13, 15%, P = 0.0114). Equal frequencies of lower and higher RASSF1A expression levels were only observed in non-small cell lung cancer (16/38, 42%). Noteworthy, an increase in expression was more common at early clinical stages of squamous cell lung cancer and adenocarcinoma, while a decrease in RASSF1A expression was more frequent at advanced clinical stages. In clear cell renal cell carcinoma, an increase in RASSF1A expression occurred more often at both early and advanced stages and was significant at advanced stages (P = 0.0094). The findings suggested tumor specificity for changes in RASSF1A expression. The observed regularities may also indicate that RASSF1A has dual functions in tumors, acting as a tumor suppressor and as a protooncogene.     

Copy number variations of chromosome 17p13.1 might be linked to high risk of lung cancer in heavy smokers

Lung cancer is the most common cause of cancer death worldwide. Smoking is known as the strongest single factor in the development of lung cancer. However, there are inherited genetic factors that cause different responses to cigarette smoking exposure among individuals. We tried to identify these differences in heavy smokers by examining copy number variations (CNVs) between lung cancer patients and healthy controls. Analysis by array comparative genomic hybridization which was tested with 20-person training set (10 lung cancer patients, 10 healthy controls) showed 26 significant (adjusted P < 0.05) clones with either copy number gains or losses. Three genes, KCTD11, FGF11, and PTPRH on chromosomal regions 17p13.1 (KCTD11 and FGF11) and 19q13.42 (PTPRH), were selected (adjusted P < 0.001) and tested by real-time quantitative PCR with 34 healthy controls and 54 lung cancer patients. KCTD11 on the chromosomal region 17p13.1 showed significant high odds ratio (OR = 16.0) in heavy smokers, implying that this is a susceptibility region for lung cancer in this group. Therefore, CNVs of 17p13.1 is a promising candidate to identify individuals with a high genetic risk for the development of lung cancer.     

Habitat-dependent advertisement call variation in the monkey frog Phyllomedusa nordestina

The acoustic adaptation hypothesis (AAH) predicts that acoustic signals are selected to propagate more efficiently in the habitat where they are normally transmitted. Several studies corroborated the AAH for primates and birds, but evidence for frogs is contentious: While most studies failed to support the AAH, recent studies have shown that within-species variation conforms to the predictions of the AAH. Herein, we test the AAH by comparing advertisement calls of Phyllomedusa nordestina from two contrasting habitats (Atlantic Rainforest and Caatinga) and by testing the influence of the amount of vegetation around calling sites on acoustic parameters of frog calls. The interval between pulses was significantly different between individuals from the Atlantic Rainforest and from the Caatinga, and the number of pulses was correlated with the amount of vegetation around calling sites. Hence, our results indicate that multiple evolutionary forces may act simultaneously on the advertisement calls of frogs.     

肺磨玻璃结节中ki-67的表达及与P53,EGFR,CEA相关性研究

目的:为探究不同病理类型的肺磨玻璃结节(ground-glass opacity,GGO)中ki-67的表达情况及其与肺癌相关标志物p53、p63、EGFR等表达的相关性。方法:收集从2012年10月至2014年10月我院胸外科收治的254例GGO病人的临床病史、影像、病理及血常规等资料予以回顾性分析。结果:Ki-67表达量从良性组(n=66),不典型腺瘤样增生(atypical adenomatous hyperplasia,AAH,n=27),到原位癌(adenocarcinoma in situ,AIS,n=11),微浸润腺癌(minimally invasive adenocarcinoma,MIA,n=108),最后到浸润性腺癌(invasive adenocarcinoma,IAC,n=42)即随着早期肺癌的演进过程不断增高。Ki-67与各标志物的相关系数为0.386(p53,P0.001)、0.227(EGFR,P=0.024)、0.441(CEA,P0.001)。通过ROC曲线分析得到ki-67来判别良恶性GGO的曲线下面积和最佳阈值,也得到了早期肺癌演进过程中ki-67阈值变化。恶性GGO组全血细胞中平均单核细胞含量低于良性组GGO,且差异有统计学意义。结论:ki-67表达量在不同病理类别的GGO中有显著性差异,且在肺癌演进过程中依次增高,可作为鉴别早期肺癌不同病理类型的参考依据和预后因子;ki-67与P53、EGFR及CEA的表达具有一定的相关性。     

Association of a new intronic polymorphism of the SOD2 gene (G1677T) with cancer

There is growing evidence of the correlation between cancer and reactive oxygen species (ROS), especially superoxide. Low expression levels of the Mn‐superoxide dismutase (SOD2) enzyme have been reported in cancer patients. Genetic variation in the regulatory regions of the SOD2 gene may increase the risk of cancer. We identified a genetic variation (G1677T, rs2Y758Y339) in the vicinity of the enhancer region located in intron 2 of the SOD2 gene that creates a potential glucocorticoid responsive element, and developed an assay to screen DNA samples of 220 individuals (73 control, 59 prostate cancer survival individuals and 88 lung cancer biopsies). There were no significant differences in the genotype frequency distribution among prostate, lung cancer and control (p = 0.074 and 0.057, respectively). However, we identified an association of T allele with a decreased risk of lung cancer (OR = 0.525, p = 0.037). The use of the G1677T polymorphism of SOD2 gene as a genetic risk marker may suggest new approaches for detection, prevention, treatment, and prognosis of cancer. Copyright © 2009 John Wiley & Sons, Ltd.