Candidate Luminal B Breast Cancer Genes Identified by Genome,Gene Expression and DNA Methylation Profiling

Breast cancers (BCs) of the luminal B subtype are estrogen receptor-positive (ER+), highly proliferative, resistant to standard therapies and have a poor prognosis. To better understand this subtype we compared DNA copy number aberrations (CNAs), DNA promoter methylation, gene expression profiles, and somatic mutations in nine selected genes, in 32 luminal B tumors with those observed in 156 BCs of the other molecular subtypes. Frequent CNAs included 8p11-p12 and 11q13.1-q13.2 amplifications, 7q11.22-q34, 8q21.12-q24.23, 12p12.3-p13.1, 12q13.11-q24.11, 14q21.1-q23.1, 17q11.1-q25.1, 20q11.23-q13.33 gains and 6q14.1-q24.2, 9p21.3-p24,3, 9q21.2, 18p11.31-p11.32 losses. A total of 237 and 101 luminal B-specific candidate oncogenes and tumor suppressor genes (TSGs) presented a deregulated expression in relation with their CNAs, including 11 genes previously reported associated with endocrine resistance. Interestingly, 88% of the potential TSGs are located within chromosome arm 6q, and seven candidate oncogenes are potential therapeutic targets. A total of 100 candidate oncogenes were validated in a public series of 5,765 BCs and the overexpression of 67 of these was associated with poor survival in luminal tumors. Twenty-four genes presented a deregulated expression in relation with a high DNA methylation level. FOXO3, PIK3CA and TP53 were the most frequent mutated genes among the nine tested. In a meta-analysis of next-generation sequencing data in 875 BCs, KCNB2 mutations were associated with luminal B cases while candidate TSGs MDN1 (6q15) and UTRN (6q24), were mutated in this subtype. In conclusion, we have reported luminal B candidate genes that may play a role in the development and/or hormone resistance of this aggressive subtype.     

An Integrative CGH,MSI and Candidate Genes Methylation Analysis of Colorectal Tumors

Background

Different DNA aberrations processes can cause colorectal cancer (CRC). Herein, we conducted a comprehensive molecular characterization of 27 CRCs from Iranian patients.

Materials and Methods

Array CGH was performed. The MSI phenotype and the methylation status of 15 genes was established using MSP. The CGH data was compared to two established lists of 41 and 68 cancer genes, respectively, and to CGH data from African Americans. A maximum parsimony cladogram based on global aberrations was established.

Results

The number of aberrations seem to depend on the MSI status. MSI-H tumors displayed the lowest number of aberrations. MSP revealed that most markers were methylated, except RNF182 gene. P16 and MLH1 genes were primarily methylated in MSI-H tumors. Seven markers with moderate to high frequency of methylation (SYNE1, MMP2, CD109, EVL, RET, LGR and PTPRD) had very low levels of chromosomal aberrations. All chromosomes were targeted by aberrations with deletions more frequent than amplifications. The most amplified markers were CD248, ERCC6, ERGIC3, GNAS, MMP2, NF1, P2RX7, SFRS6, SLC29A1 and TBX22. Most deletions were noted for ADAM29, CHL1, CSMD3, FBXW7, GALNS, MMP2, NF1, PRKD1, SMAD4 and TP53. Aberrations targeting chromosome X were primarily amplifications in male patients and deletions in female patients. A finding similar to what we reported for African American CRC patients.

Conclusion

This first comprehensive analysis of CRC Iranian tumors reveals a high MSI rate. The MSI tumors displayed the lowest level of chromosomal aberrations but high frequency of methylation. The MSI-L were predominantly targeted with chromosomal instability in a way similar to the MSS tumors. The global chromosomal aberration profiles showed many similarities with other populations but also differences that might allow a better understanding of CRC''s clinico-pathological specifics in this population.     

DNA甲基化与癌症

DNA甲基化是重要的表观遗传修饰,主要发生在DNA的CpG岛. DNA的甲基化通过DNA甲基转移酶（DNA methyltransferases, DNMTs）完成. DNA甲基化参与了细胞分化、基因组稳定性、X染色体失活、基因印记等多种细胞生物学过程.单基因水平及基因组范围内的DNA甲基化改变在肿瘤发生发展中亦发挥重要作用. 抑癌基因的异常甲基化引起的表达抑制,可导致肿瘤细胞的增殖失控和侵袭转移,并参与肿瘤组织的血管生成过程.在许多肿瘤的研究中都发现了基因组整体DNA低甲基化所导致的染色体不稳定性. 本文从DNA的异常高甲基化和低甲基化两方面论述了DNA甲基化在细胞恶变发生发展过程中的改变及其影响,并阐述了DNA甲基化改变在肿瘤诊断和治疗中的作用.     

水稻虫害诱导相关基因实时定量PCR中内参基因的选择

实时定量PCR技术广泛应用于植物功能基因转录水平变化的研究, 选择合适的内参基因进行相对定量分析是实验结果准确的关键因素。通过分析5个常用的内参基因(eEF-1α、18S rRNA、25S rRNA、Actin和UBQ5)在水稻(Oryza sativa)经过各种处理后表达的稳定性, 结果表明, 水稻经过机械损伤处理后eEF-1α基因的表达最稳定; 二化螟处理后25S rRNA基因的表达最为稳定; 稻纵卷叶螟处理后Actin基因的表达最稳定; 两种刺吸式口器昆虫褐飞虱和白背飞虱危害后, UBQ5基因的表达最稳定。同时, 利用OsHI-LOX基因在不同处理后的表达来评价这些内参基因。研究结果为水稻虫害诱导实时定量PCR分析中内参基因的选择提供了理论依据。     

DNA Methylation Markers in Lung Cancer

Lung cancer is the most common cancer and the leading cause of cancer-related morbidity and mortality worldwide. As early symptoms of lung cancer are minimal and non-specific, many patients are diagnosed at an advanced stage. Despite a concerted effort to diagnose lung cancer early, no biomarkers that can be used for lung cancer screening and prognosis prediction have been established so far. As global DNA demethylation and gene-specific promoter DNA methylation are present in lung cancer, DNA methylation biomarkers have become a major area of research as potential alternative diagnostic methods to detect lung cancer at an early stage. This review summarizes the emerging DNA methylation changes in lung cancer tumorigenesis, focusing on biomarkers for early detection and their potential clinical applications in lung cancer.     

DNA异常甲基化在宫颈癌中的研究进展

长期以来人们一直认为基因突变或基因缺失参与肿瘤的形成。近年来众多研究表明,表观遗传修饰对肿瘤的发展也具有非常重要的意义,它的主要表现形式有DNA甲基化、组蛋白修饰、微小RNA调节、染色质重组等。DNA异常甲基化可通过影响染色质结构、癌基因及抑癌基因表达而参与肿瘤的形成。了解目前宫颈癌中DNA甲基化的研究进展不仅有助于宫颈癌的早期诊断,对其分子靶向治疗及预后评估亦显示出良好的应用前景。     

DNA异常甲基化在宫颈癌中的研究进展

长期以来人们一直认为基因突变或基因缺失参与肿瘤的形成。近年来众多研究表明,表观遗传修饰对肿瘤的发展也具有非常重要的意义,它的主要表现形式有DNA甲基化、组蛋白修饰、微小RNA调节、染色质重组等。DNA异常甲基化可通过影响染色质结构、癌基因及抑癌基因表达而参与肿瘤的形成。了解目前宫颈癌中DNA甲基化的研究进展不仅有助于宫颈癌的早期诊断,对其分子靶向治疗及预后评估亦显示出良好的应用前景。     

FHIT基因在宫颈癌细胞中的表达及其甲基化调控

目的：分析FHIT基因在宫颈癌细胞中表达情况以及甲基化的调控情况。方法：对RJC-1、SiHa、CS1213以及C4-1细胞进行培养,提取这些细胞的DNA并经过亚硫酸氢盐修饰,进行PCR反应和产物的检测。分析FHIT基因在宫颈癌细胞中表达情况以及甲基化的调控情况。结果：RJC-1、CS1213细胞仅有甲基化引物扩增出了目的条带,为完全甲基化状态。其他细胞则是甲基特异性引物与非甲基特异性引物共同扩增出73bp的目的条带,其状态为甲基化杂合性。通过5-aza-CdR处理细胞后,通过实时定量PCR检测FHIT mRNA的表达,显示处理后各种细胞中的FHIT mRNA的表达升高。结论：FHIT基因的甲基化是其表达下调的重要机制之一,是临床研究宫颈癌细胞的重要方向之一。     

Eleven Candidate Susceptibility Genes for Common Familial Colorectal Cancer

Hereditary factors are presumed to play a role in one third of colorectal cancer (CRC) cases. However, in the majority of familial CRC cases the genetic basis of predisposition remains unexplained. This is particularly true for families with few affected individuals. To identify susceptibility genes for this common phenotype, we examined familial cases derived from a consecutive series of 1514 Finnish CRC patients. Ninety-six familial CRC patients with no previous diagnosis of a hereditary CRC syndrome were included in the analysis. Eighty-six patients had one affected first-degree relative, and ten patients had two or more. Exome sequencing was utilized to search for genes harboring putative loss-of-function variants, because such alterations are likely candidates for disease-causing mutations. Eleven genes with rare truncating variants in two or three familial CRC cases were identified: UACA, SFXN4, TWSG1, PSPH, NUDT7, ZNF490, PRSS37, CCDC18, PRADC1, MRPL3, and AKR1C4. Loss of heterozygosity was examined in all respective cancer samples, and was detected in seven occasions involving four of the candidate genes. In all seven occasions the wild-type allele was lost (P = 0.0078) providing additional evidence that these eleven genes are likely to include true culprits. The study provides a set of candidate predisposition genes which may explain a subset of common familial CRC. Additional genetic validation in other populations is required to provide firm evidence for causality, as well as to characterize the natural history of the respective phenotypes.     

Identification of Novel Candidate Genes for Early-Onset Colorectal Cancer Susceptibility

Approximately 25–30% of colorectal cancer (CRC) cases are expected to result from a genetic predisposition, but in only 5–10% of these cases highly penetrant germline mutations are found. The remaining CRC heritability is still unexplained, and may be caused by a hitherto-undefined set of rare variants with a moderately penetrant risk. Here we aimed to identify novel risk factors for early-onset CRC using whole-exome sequencing, which was performed on a cohort of CRC individuals (n = 55) with a disease onset before 45 years of age. We searched for genes that were recurrently affected by rare variants (minor allele frequency ≤0.001) with potentially damaging effects and, subsequently, re-sequenced the candidate genes in a replication cohort of 174 early-onset or familial CRC individuals. Two functionally relevant genes with low frequency variants with potentially damaging effects, PTPN12 and LRP6, were found in at least three individuals. The protein tyrosine phosphatase PTP-PEST, encoded by PTPN12, is a regulator of cell motility and LRP6 is a component of the WNT-FZD-LRP5-LRP6 complex that triggers WNT signaling. All variants in LRP6 were identified in individuals with an extremely early-onset of the disease (≤30 years of age), and two of the three variants showed increased WNT signaling activity in vitro. In conclusion, we present PTPN12 and LRP6 as novel candidates contributing to the heterogeneous susceptibility to CRC.     

乳腺癌相关基因的DNA甲基化

乳腺癌是女性最常见的恶性肿瘤之一。DNA甲基化作为哺乳动物细胞基因组修饰和表达调控的表观遗传学方式,在肿瘤的发生发展过程中总体水平降低,但同时又伴随某些基因的高甲基化。在乳腺癌中,多种关键基因的表达缺失都与其CpG岛高甲基化有关。     

肺癌与DNA 甲基化研究的进展

DNA甲基化是表观遗传学研究的重要内容。其本质是在甲基转移酶的催化下,DNA的CG两个核苷酸的胞嘧啶被选择性地添加甲基,形成5’甲基胞嘧啶的过程。CpG岛是DNA甲基化常发生的部位。CpG岛指基因组中长度为300～3000 bp的富含CpG二核苷酸的一些区域,主要存在于基因的5’区域。以往的研究表明,肺癌的发生常与CpG岛的异常甲基化有关。多基因异常的甲基化常为肿瘤发生的重要机制。近年来,研究比较热门的基因有p16、RASSF1A、CDH1、CDH13、FHTI、TMS1/ASC等。研究集中在肺癌组织与癌旁组织甲基化频率的统计分析,以及对于血液,痰液,肺泡灌洗液发生甲基化频率的统计分析。对于肺癌相关抑癌基因甲基化的研究,为肺癌患者的早期诊断提供思路,并为治疗开辟新的方向。去甲基化治疗虽研究较少,但目前已取得一定进展。     

DNA甲基化与膀胱癌的研究进展

DNA甲基化与膀胱癌的发生有密切的关系,是抑癌基因失活的一个重要方式,有可能成为膀胱癌诊断的分子标志物.去甲基化有望成为膀胱癌治疗新方法.同时甲基化分析技术发展迅速,包括寡核苷酸探针微阵列在内的甲基化芯片技术已成为目前甲基化检测的主要方法.本文就其相关进展进行综述.     

DNA Methyltransferase Candidate Polymorphisms,Imprinting Methylation,and Birth Outcome

Background

Birth weight and prematurity are important obstetric outcomes linked to lifelong health. We studied a large birth cohort to look for evidence of epigenetic involvement in birth outcomes.

Methods

We investigated the association between birth weight, length, placental weight and duration of gestation and four candidate variants in 1,236 mothers and 1,073 newborns; DNMT1 (rs2162560), DNMT3A (rs734693), DNMT3B (rs2424913) and DNMT3L (rs7354779). We measured methylation of LINE1 and the imprinted genes, PEG3, SNRPN, and IGF2, in cord blood.

Results

The minor DNMT3L allele in the baby was associated with higher birth weight (+54 95% CI 10,99 g; p = 0.016), birth length (+0.23 95% CI 0.04,0.42 cm; p = 0.017), placental weight, (+18 95% CI 3,33 g; p = 0.017), and reduced risk of being in the lowest birth weight decile (p = 0.018) or requiring neonatal care (p = 0.039). The DNMT3B minor allele in the mother was associated with an increased risk of prematurity (p = 0.001). Placental size was related to PEG3 (p<0.001) and IGF2 (p<0.001) methylation. Birth weight was related to LINE1 and IGF2 methylation but only at p = 0.052. The risk of requiring neonatal treatment was related to LINE1 (p = 0.010) and SNRPN (p = 0.001) methylation. PEG3 methylation was influenced by baby DNMT3A genotype (p = 0.012) and LINE1 by baby 3B genotype (p = 0.044). Maternal DNMT3L genotype was related to IGF2 methylation in the cord blood but this effect was only seen in carriers of the minor frequency allele (p = 0.050).

Conclusions

The results here suggest that epigenetic processes are linked birth outcome and health in early life. Our emerging understanding of the role of epigenetics in health and biological function across the lifecourse suggests that these early epigenetic events could have longer term implications.     

Methylation Profile of Several Tumor Suppressor Genes in Non-Small-Cell Lung Cancer

Multiplex methylation-sensitive PCR was employed in studying the methylation of CpG islands in the RB1, p16/CDKN2A, p15/CDKN2B, p14/ARF, CDH1, HIC1, and N33 5 regions in non-small cell lung cancer (51 tumors). Methylation was observed for the two suppressor genes involved in controlling the cell cycle through the Cdk–Rb–E2F signaling pathway, RB1 (10/51, 19%) and p16 (20/51, 39%). The highest methylation frequencies were established for CDH1 (72%) and HIC1 (82%). The CpG islands of p14 and p15 proved to be nonmethylated. At least one gene was methylated in 90% (46/51) tumors and no gene, in 10% (5/51) tumors. In addition, the genes were tested for methylation in peripheral blood lymphocytes of healthy subjects. Methylation frequency significantly differed between tumors and normal cells in the case of RB1, p16, CDH1, HIC1, and N33. Gene methylation frequency was tested for association with histological type of the tumor and stage of tumor progression. Methylation index of a panel of tumor suppressor genes was established for groups of tumors varying in clinical and morphological parameters.